Starting phenix.real_space_refine on Sat Dec 28 03:34:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x9p_38178/12_2024/8x9p_38178.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x9p_38178/12_2024/8x9p_38178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x9p_38178/12_2024/8x9p_38178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x9p_38178/12_2024/8x9p_38178.map" model { file = "/net/cci-nas-00/data/ceres_data/8x9p_38178/12_2024/8x9p_38178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x9p_38178/12_2024/8x9p_38178.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 4835 2.51 5 N 1307 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7669 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3423 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418} Chain: "B" Number of atoms: 3359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3359 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 887 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 2, 'TRANS': 104} Time building chain proxies: 4.89, per 1000 atoms: 0.64 Number of scatterers: 7669 At special positions: 0 Unit cell: (106.24, 79.68, 99.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1474 8.00 N 1307 7.00 C 4835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 5 sheets defined 57.5% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.261A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.606A pdb=" N PHE A 87 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.638A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 162 removed outlier: 4.333A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.504A pdb=" N SER A 178 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.541A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.896A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.726A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.380A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 438 removed outlier: 3.975A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.506A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.511A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 109 through 127 removed outlier: 4.925A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.331A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 4.592A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.853A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.706A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.782A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.587A pdb=" N GLY B 400 " --> pdb=" O HIS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 4.089A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 256 Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 303 through 334 removed outlier: 3.574A pdb=" N LEU C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN C 317 " --> pdb=" O MET C 313 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.804A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 7.148A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.386A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 166 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.860A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 421 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2499 1.34 - 1.46: 1288 1.46 - 1.58: 3969 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 7839 Sorted by residual: bond pdb=" CB ILE B 16 " pdb=" CG2 ILE B 16 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.65e+00 bond pdb=" CG1 ILE B 16 " pdb=" CD1 ILE B 16 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.62e+00 bond pdb=" CB MET B 233 " pdb=" CG MET B 233 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.34e+00 bond pdb=" C CYS A 4 " pdb=" N ILE A 5 " ideal model delta sigma weight residual 1.335 1.314 0.021 1.41e-02 5.03e+03 2.27e+00 bond pdb=" CG1 ILE A 188 " pdb=" CD1 ILE A 188 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 ... (remaining 7834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 10460 2.32 - 4.64: 130 4.64 - 6.96: 21 6.96 - 9.28: 6 9.28 - 11.61: 2 Bond angle restraints: 10619 Sorted by residual: angle pdb=" N VAL B 180 " pdb=" CA VAL B 180 " pdb=" C VAL B 180 " ideal model delta sigma weight residual 113.20 109.77 3.43 9.60e-01 1.09e+00 1.28e+01 angle pdb=" CA TRP C 311 " pdb=" CB TRP C 311 " pdb=" CG TRP C 311 " ideal model delta sigma weight residual 113.60 107.01 6.59 1.90e+00 2.77e-01 1.20e+01 angle pdb=" CA LEU B 151 " pdb=" CB LEU B 151 " pdb=" CG LEU B 151 " ideal model delta sigma weight residual 116.30 127.91 -11.61 3.50e+00 8.16e-02 1.10e+01 angle pdb=" CA GLN C 285 " pdb=" CB GLN C 285 " pdb=" CG GLN C 285 " ideal model delta sigma weight residual 114.10 120.67 -6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB MET B 233 " pdb=" CG MET B 233 " pdb=" SD MET B 233 " ideal model delta sigma weight residual 112.70 102.95 9.75 3.00e+00 1.11e-01 1.06e+01 ... (remaining 10614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4070 17.99 - 35.99: 487 35.99 - 53.98: 92 53.98 - 71.98: 23 71.98 - 89.97: 6 Dihedral angle restraints: 4678 sinusoidal: 1874 harmonic: 2804 Sorted by residual: dihedral pdb=" CA MET B 1 " pdb=" C MET B 1 " pdb=" N ARG B 2 " pdb=" CA ARG B 2 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLN B 384 " pdb=" C GLN B 384 " pdb=" N PHE B 385 " pdb=" CA PHE B 385 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASN B 195 " pdb=" CB ASN B 195 " pdb=" CG ASN B 195 " pdb=" OD1 ASN B 195 " ideal model delta sinusoidal sigma weight residual -90.00 -163.81 73.81 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 4675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 832 0.045 - 0.089: 255 0.089 - 0.134: 65 0.134 - 0.178: 5 0.178 - 0.223: 1 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CB ILE B 16 " pdb=" CA ILE B 16 " pdb=" CG1 ILE B 16 " pdb=" CG2 ILE B 16 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 363 " pdb=" CA VAL A 363 " pdb=" CG1 VAL A 363 " pdb=" CG2 VAL A 363 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA MET C 313 " pdb=" N MET C 313 " pdb=" C MET C 313 " pdb=" CB MET C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 1155 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 286 " -0.025 2.00e-02 2.50e+03 1.85e-02 6.00e+00 pdb=" CG PHE C 286 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 286 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 286 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 286 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 286 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 316 " -0.018 2.00e-02 2.50e+03 1.83e-02 5.83e+00 pdb=" CG PHE C 316 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 316 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 316 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 316 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 316 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 316 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 385 " 0.015 2.00e-02 2.50e+03 1.46e-02 3.71e+00 pdb=" CG PHE B 385 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 385 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 385 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 385 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 385 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 385 " 0.001 2.00e-02 2.50e+03 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 225 2.70 - 3.25: 8246 3.25 - 3.80: 13014 3.80 - 4.35: 16607 4.35 - 4.90: 27070 Nonbonded interactions: 65162 Sorted by model distance: nonbonded pdb=" OG1 THR B 285 " pdb=" OE1 GLU B 288 " model vdw 2.145 3.040 nonbonded pdb=" N GLU B 407 " pdb=" OE1 GLU B 407 " model vdw 2.219 3.120 nonbonded pdb=" OG SER B 145 " pdb=" OG SER B 188 " model vdw 2.228 3.040 nonbonded pdb=" O GLY B 10 " pdb=" ND2 ASN B 14 " model vdw 2.232 3.120 nonbonded pdb=" NE2 GLN A 301 " pdb=" O CYS A 305 " model vdw 2.257 3.120 ... (remaining 65157 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.220 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7839 Z= 0.262 Angle : 0.671 11.605 10619 Z= 0.352 Chirality : 0.044 0.223 1158 Planarity : 0.004 0.037 1396 Dihedral : 16.057 89.973 2880 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.12 % Allowed : 21.44 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 967 helix: 0.63 (0.23), residues: 479 sheet: 0.80 (0.47), residues: 135 loop : -0.06 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 311 HIS 0.004 0.001 HIS A 406 PHE 0.042 0.002 PHE C 316 TYR 0.011 0.001 TYR A 399 ARG 0.003 0.000 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6177 (tmm) cc_final: 0.5879 (tmm) REVERT: A 199 ASP cc_start: 0.7970 (t0) cc_final: 0.7658 (t0) REVERT: A 217 LEU cc_start: 0.8496 (mt) cc_final: 0.7738 (mt) REVERT: A 272 TYR cc_start: 0.8026 (t80) cc_final: 0.7676 (t80) REVERT: A 313 MET cc_start: 0.7696 (mmm) cc_final: 0.7325 (tmm) REVERT: B 65 LEU cc_start: 0.8115 (mm) cc_final: 0.7566 (mm) REVERT: B 207 LEU cc_start: 0.7547 (mt) cc_final: 0.7154 (mt) REVERT: B 226 ASN cc_start: 0.8065 (m-40) cc_final: 0.7558 (m110) REVERT: B 257 MET cc_start: 0.7956 (tpp) cc_final: 0.7233 (mmt) REVERT: B 364 SER cc_start: 0.8579 (p) cc_final: 0.8342 (m) REVERT: B 406 MET cc_start: 0.9029 (mmm) cc_final: 0.8805 (mmt) REVERT: C 231 VAL cc_start: 0.7931 (p) cc_final: 0.7357 (m) REVERT: C 244 LYS cc_start: 0.8626 (ptmt) cc_final: 0.8295 (pttt) REVERT: C 267 LEU cc_start: 0.8871 (mm) cc_final: 0.8431 (mm) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2073 time to fit residues: 55.8378 Evaluate side-chains 135 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 195 ASN B 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7839 Z= 0.273 Angle : 0.657 11.805 10619 Z= 0.345 Chirality : 0.045 0.175 1158 Planarity : 0.005 0.051 1396 Dihedral : 4.154 16.551 1055 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.75 % Allowed : 20.72 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 967 helix: 0.52 (0.23), residues: 484 sheet: 0.60 (0.45), residues: 134 loop : -0.14 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 311 HIS 0.009 0.002 HIS A 309 PHE 0.034 0.002 PHE C 316 TYR 0.014 0.001 TYR A 24 ARG 0.005 0.001 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.8012 (t0) cc_final: 0.7720 (t0) REVERT: A 213 CYS cc_start: 0.8779 (t) cc_final: 0.8549 (t) REVERT: A 272 TYR cc_start: 0.8084 (t80) cc_final: 0.7799 (t80) REVERT: B 209 ASP cc_start: 0.8394 (t0) cc_final: 0.7964 (t0) REVERT: B 226 ASN cc_start: 0.8146 (m-40) cc_final: 0.7808 (m-40) REVERT: B 364 SER cc_start: 0.8588 (p) cc_final: 0.8329 (m) REVERT: C 241 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7275 (mm-30) REVERT: C 244 LYS cc_start: 0.8683 (ptmt) cc_final: 0.8424 (pttm) REVERT: C 250 PHE cc_start: 0.8332 (m-80) cc_final: 0.8040 (m-80) REVERT: C 267 LEU cc_start: 0.8898 (mm) cc_final: 0.8449 (mm) outliers start: 23 outliers final: 16 residues processed: 173 average time/residue: 0.1927 time to fit residues: 45.7624 Evaluate side-chains 151 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 260 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7839 Z= 0.208 Angle : 0.606 8.199 10619 Z= 0.313 Chirality : 0.043 0.166 1158 Planarity : 0.004 0.067 1396 Dihedral : 4.061 16.382 1055 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.71 % Allowed : 19.76 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 967 helix: 0.65 (0.23), residues: 490 sheet: 0.63 (0.45), residues: 127 loop : -0.22 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 311 HIS 0.009 0.001 HIS B 227 PHE 0.026 0.002 PHE C 316 TYR 0.022 0.001 TYR A 24 ARG 0.005 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASN cc_start: 0.8041 (p0) cc_final: 0.7624 (p0) REVERT: A 199 ASP cc_start: 0.8033 (t0) cc_final: 0.7778 (t0) REVERT: A 213 CYS cc_start: 0.8714 (t) cc_final: 0.8391 (t) REVERT: A 228 ASN cc_start: 0.7956 (m110) cc_final: 0.7739 (m-40) REVERT: A 272 TYR cc_start: 0.8020 (t80) cc_final: 0.7812 (t80) REVERT: B 73 MET cc_start: 0.5044 (mpt) cc_final: 0.4537 (mpp) REVERT: B 207 LEU cc_start: 0.7914 (mt) cc_final: 0.7358 (mt) REVERT: B 226 ASN cc_start: 0.8172 (m-40) cc_final: 0.7819 (m-40) REVERT: B 364 SER cc_start: 0.8632 (p) cc_final: 0.8373 (m) REVERT: B 406 MET cc_start: 0.9071 (mmm) cc_final: 0.8762 (mmm) REVERT: C 250 PHE cc_start: 0.8388 (m-80) cc_final: 0.8159 (m-10) REVERT: C 260 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5791 (tp) REVERT: C 267 LEU cc_start: 0.8833 (mm) cc_final: 0.8437 (mm) outliers start: 31 outliers final: 16 residues processed: 174 average time/residue: 0.2062 time to fit residues: 48.6313 Evaluate side-chains 148 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 311 TRP Chi-restraints excluded: chain C residue 320 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7839 Z= 0.233 Angle : 0.619 11.821 10619 Z= 0.317 Chirality : 0.043 0.181 1158 Planarity : 0.004 0.065 1396 Dihedral : 4.163 21.210 1055 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.59 % Allowed : 20.72 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 967 helix: 0.67 (0.23), residues: 489 sheet: 0.39 (0.45), residues: 132 loop : -0.23 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 311 HIS 0.006 0.001 HIS A 107 PHE 0.020 0.002 PHE B 408 TYR 0.019 0.001 TYR A 24 ARG 0.005 0.000 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.8034 (t0) cc_final: 0.7762 (t0) REVERT: A 213 CYS cc_start: 0.8727 (t) cc_final: 0.8398 (t) REVERT: A 217 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8145 (mt) REVERT: A 228 ASN cc_start: 0.8011 (m110) cc_final: 0.7758 (m-40) REVERT: A 272 TYR cc_start: 0.8026 (t80) cc_final: 0.7822 (t80) REVERT: B 73 MET cc_start: 0.5018 (mpt) cc_final: 0.4686 (mpp) REVERT: B 207 LEU cc_start: 0.7846 (mt) cc_final: 0.7283 (mt) REVERT: B 226 ASN cc_start: 0.8171 (m-40) cc_final: 0.7773 (m110) REVERT: B 364 SER cc_start: 0.8733 (p) cc_final: 0.8411 (m) REVERT: B 406 MET cc_start: 0.9135 (mmm) cc_final: 0.8795 (mmm) REVERT: C 250 PHE cc_start: 0.8412 (m-10) cc_final: 0.8161 (m-10) REVERT: C 252 TRP cc_start: 0.7933 (m100) cc_final: 0.7595 (m100) REVERT: C 267 LEU cc_start: 0.8932 (mm) cc_final: 0.8500 (mm) outliers start: 30 outliers final: 24 residues processed: 164 average time/residue: 0.2014 time to fit residues: 45.6143 Evaluate side-chains 156 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 311 TRP Chi-restraints excluded: chain C residue 320 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.2980 chunk 52 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7839 Z= 0.187 Angle : 0.608 11.833 10619 Z= 0.309 Chirality : 0.042 0.215 1158 Planarity : 0.004 0.053 1396 Dihedral : 4.049 15.236 1055 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.95 % Allowed : 20.24 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.27), residues: 967 helix: 0.66 (0.23), residues: 486 sheet: 0.43 (0.45), residues: 132 loop : -0.19 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 311 HIS 0.005 0.001 HIS A 107 PHE 0.023 0.001 PHE B 408 TYR 0.045 0.001 TYR A 24 ARG 0.008 0.000 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8528 (m-80) cc_final: 0.8313 (m-80) REVERT: A 199 ASP cc_start: 0.7984 (t0) cc_final: 0.7726 (t0) REVERT: A 213 CYS cc_start: 0.8668 (t) cc_final: 0.8334 (t) REVERT: A 217 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 228 ASN cc_start: 0.8144 (m110) cc_final: 0.7880 (m110) REVERT: B 73 MET cc_start: 0.4997 (mpt) cc_final: 0.4701 (mpp) REVERT: B 207 LEU cc_start: 0.7736 (mt) cc_final: 0.7305 (mt) REVERT: B 226 ASN cc_start: 0.8155 (m-40) cc_final: 0.7853 (m110) REVERT: B 364 SER cc_start: 0.8727 (p) cc_final: 0.8391 (m) REVERT: B 406 MET cc_start: 0.9167 (mmm) cc_final: 0.8769 (mmm) REVERT: C 250 PHE cc_start: 0.8400 (m-10) cc_final: 0.8112 (m-10) REVERT: C 260 ILE cc_start: 0.6335 (OUTLIER) cc_final: 0.5776 (tp) REVERT: C 267 LEU cc_start: 0.8894 (mm) cc_final: 0.8414 (mm) REVERT: C 312 ASP cc_start: 0.8737 (m-30) cc_final: 0.8475 (t0) outliers start: 33 outliers final: 22 residues processed: 171 average time/residue: 0.1963 time to fit residues: 48.2817 Evaluate side-chains 156 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS C 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7839 Z= 0.191 Angle : 0.609 10.213 10619 Z= 0.312 Chirality : 0.042 0.228 1158 Planarity : 0.004 0.053 1396 Dihedral : 3.959 14.992 1055 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.47 % Allowed : 22.04 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.27), residues: 967 helix: 0.75 (0.23), residues: 483 sheet: 0.37 (0.46), residues: 132 loop : -0.21 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP C 311 HIS 0.005 0.001 HIS A 107 PHE 0.019 0.001 PHE B 408 TYR 0.034 0.001 TYR A 24 ARG 0.007 0.000 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7965 (t0) cc_final: 0.7711 (t0) REVERT: A 213 CYS cc_start: 0.8674 (t) cc_final: 0.8333 (t) REVERT: A 217 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8138 (mt) REVERT: A 228 ASN cc_start: 0.8157 (m110) cc_final: 0.7887 (m110) REVERT: B 1 MET cc_start: 0.6487 (pmm) cc_final: 0.6266 (pmm) REVERT: B 73 MET cc_start: 0.5016 (mpt) cc_final: 0.4748 (mpp) REVERT: B 207 LEU cc_start: 0.7686 (mt) cc_final: 0.7249 (mt) REVERT: B 226 ASN cc_start: 0.8177 (m-40) cc_final: 0.7882 (m110) REVERT: B 364 SER cc_start: 0.8693 (p) cc_final: 0.8389 (m) REVERT: B 383 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7307 (mp0) REVERT: B 406 MET cc_start: 0.9158 (mmm) cc_final: 0.8815 (mmm) REVERT: C 250 PHE cc_start: 0.8452 (m-10) cc_final: 0.8167 (m-10) REVERT: C 267 LEU cc_start: 0.8913 (mm) cc_final: 0.8445 (mm) outliers start: 29 outliers final: 22 residues processed: 159 average time/residue: 0.1696 time to fit residues: 37.8833 Evaluate side-chains 148 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 245 GLN C 229 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7839 Z= 0.287 Angle : 0.659 10.480 10619 Z= 0.342 Chirality : 0.043 0.237 1158 Planarity : 0.004 0.054 1396 Dihedral : 4.144 16.772 1055 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.59 % Allowed : 22.51 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 967 helix: 0.71 (0.23), residues: 480 sheet: 0.16 (0.46), residues: 132 loop : -0.29 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.003 TRP C 311 HIS 0.007 0.001 HIS A 107 PHE 0.018 0.002 PHE B 408 TYR 0.042 0.002 TYR A 24 ARG 0.006 0.000 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7947 (t0) cc_final: 0.7746 (t0) REVERT: A 213 CYS cc_start: 0.8716 (t) cc_final: 0.8354 (t) REVERT: A 224 TYR cc_start: 0.3948 (OUTLIER) cc_final: 0.1869 (m-80) REVERT: A 228 ASN cc_start: 0.8191 (m110) cc_final: 0.7899 (m110) REVERT: B 1 MET cc_start: 0.6704 (pmm) cc_final: 0.6470 (pmm) REVERT: B 73 MET cc_start: 0.5220 (mpt) cc_final: 0.4903 (mpp) REVERT: B 207 LEU cc_start: 0.7965 (mt) cc_final: 0.7351 (mt) REVERT: B 364 SER cc_start: 0.8781 (p) cc_final: 0.8409 (m) REVERT: B 383 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7346 (mp0) REVERT: B 406 MET cc_start: 0.9201 (mmm) cc_final: 0.8893 (mmm) REVERT: B 412 GLU cc_start: 0.8280 (pp20) cc_final: 0.7734 (pp20) REVERT: C 250 PHE cc_start: 0.8500 (m-10) cc_final: 0.8215 (m-10) REVERT: C 267 LEU cc_start: 0.9016 (mm) cc_final: 0.8573 (mm) outliers start: 30 outliers final: 25 residues processed: 153 average time/residue: 0.1686 time to fit residues: 37.1385 Evaluate side-chains 154 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.0770 chunk 83 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN B 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7839 Z= 0.211 Angle : 0.643 11.390 10619 Z= 0.326 Chirality : 0.043 0.246 1158 Planarity : 0.004 0.051 1396 Dihedral : 4.103 16.582 1055 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.83 % Allowed : 22.63 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 967 helix: 0.72 (0.23), residues: 479 sheet: 0.08 (0.47), residues: 123 loop : -0.38 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP C 311 HIS 0.005 0.001 HIS A 107 PHE 0.017 0.001 PHE B 408 TYR 0.041 0.001 TYR A 24 ARG 0.006 0.000 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 CYS cc_start: 0.8702 (t) cc_final: 0.8347 (t) REVERT: A 224 TYR cc_start: 0.4249 (OUTLIER) cc_final: 0.2136 (m-80) REVERT: A 228 ASN cc_start: 0.8207 (m110) cc_final: 0.7915 (m110) REVERT: A 313 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6181 (tmm) REVERT: B 19 LYS cc_start: 0.9021 (tptm) cc_final: 0.8676 (tppt) REVERT: B 73 MET cc_start: 0.5196 (mpt) cc_final: 0.4695 (mpp) REVERT: B 207 LEU cc_start: 0.7862 (mt) cc_final: 0.7279 (mt) REVERT: B 226 ASN cc_start: 0.8244 (m-40) cc_final: 0.7813 (m110) REVERT: B 363 MET cc_start: 0.7939 (tpp) cc_final: 0.7643 (tpp) REVERT: B 364 SER cc_start: 0.8727 (p) cc_final: 0.8340 (m) REVERT: B 383 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7313 (mp0) REVERT: B 389 PHE cc_start: 0.8216 (t80) cc_final: 0.7985 (m-80) REVERT: B 406 MET cc_start: 0.9204 (mmm) cc_final: 0.8961 (mmm) REVERT: C 250 PHE cc_start: 0.8477 (m-10) cc_final: 0.8185 (m-10) REVERT: C 267 LEU cc_start: 0.9000 (mm) cc_final: 0.8565 (mm) outliers start: 32 outliers final: 25 residues processed: 162 average time/residue: 0.1737 time to fit residues: 39.7924 Evaluate side-chains 152 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7839 Z= 0.266 Angle : 0.689 12.043 10619 Z= 0.352 Chirality : 0.044 0.232 1158 Planarity : 0.004 0.055 1396 Dihedral : 4.196 17.848 1055 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.59 % Allowed : 22.63 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 967 helix: 0.59 (0.23), residues: 480 sheet: -0.05 (0.47), residues: 123 loop : -0.36 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 311 HIS 0.009 0.001 HIS B 227 PHE 0.016 0.002 PHE B 408 TYR 0.037 0.002 TYR A 24 ARG 0.006 0.000 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 CYS cc_start: 0.8722 (t) cc_final: 0.8325 (t) REVERT: A 224 TYR cc_start: 0.3558 (OUTLIER) cc_final: 0.1348 (m-80) REVERT: A 228 ASN cc_start: 0.8237 (m110) cc_final: 0.7937 (m110) REVERT: A 313 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.6136 (tmm) REVERT: B 19 LYS cc_start: 0.9038 (tptm) cc_final: 0.8717 (tppt) REVERT: B 73 MET cc_start: 0.5367 (mpt) cc_final: 0.4842 (mpp) REVERT: B 207 LEU cc_start: 0.8022 (mt) cc_final: 0.7426 (mt) REVERT: B 226 ASN cc_start: 0.8283 (m-40) cc_final: 0.7823 (m110) REVERT: B 299 MET cc_start: 0.7951 (mmt) cc_final: 0.7737 (mmt) REVERT: B 364 SER cc_start: 0.8756 (p) cc_final: 0.8392 (m) REVERT: C 250 PHE cc_start: 0.8485 (m-10) cc_final: 0.8235 (m-10) REVERT: C 267 LEU cc_start: 0.9079 (mm) cc_final: 0.8632 (mm) REVERT: C 311 TRP cc_start: 0.8842 (m100) cc_final: 0.8515 (m-10) outliers start: 30 outliers final: 27 residues processed: 156 average time/residue: 0.1703 time to fit residues: 37.3033 Evaluate side-chains 158 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7839 Z= 0.215 Angle : 0.702 12.220 10619 Z= 0.355 Chirality : 0.044 0.236 1158 Planarity : 0.004 0.054 1396 Dihedral : 4.104 17.004 1055 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 23.95 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 967 helix: 0.53 (0.23), residues: 480 sheet: 0.15 (0.48), residues: 119 loop : -0.35 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP C 311 HIS 0.013 0.001 HIS B 227 PHE 0.029 0.002 PHE B 270 TYR 0.031 0.001 TYR A 24 ARG 0.005 0.000 ARG B 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 CYS cc_start: 0.8693 (t) cc_final: 0.8288 (t) REVERT: A 224 TYR cc_start: 0.4157 (OUTLIER) cc_final: 0.2026 (m-80) REVERT: A 228 ASN cc_start: 0.8230 (m110) cc_final: 0.7932 (m110) REVERT: A 351 PHE cc_start: 0.6312 (p90) cc_final: 0.5848 (p90) REVERT: B 19 LYS cc_start: 0.9001 (tptm) cc_final: 0.8653 (tppt) REVERT: B 73 MET cc_start: 0.5374 (OUTLIER) cc_final: 0.5076 (mpp) REVERT: B 207 LEU cc_start: 0.7914 (mt) cc_final: 0.7341 (mt) REVERT: B 226 ASN cc_start: 0.8297 (m-40) cc_final: 0.7835 (m110) REVERT: B 267 MET cc_start: 0.7924 (ptp) cc_final: 0.7721 (mtm) REVERT: B 364 SER cc_start: 0.8594 (p) cc_final: 0.8334 (m) REVERT: B 389 PHE cc_start: 0.8124 (t80) cc_final: 0.7896 (m-80) REVERT: C 250 PHE cc_start: 0.8512 (m-10) cc_final: 0.8275 (m-10) REVERT: C 267 LEU cc_start: 0.9010 (mm) cc_final: 0.8572 (mm) REVERT: C 279 MET cc_start: 0.8235 (mmt) cc_final: 0.7986 (mmm) outliers start: 25 outliers final: 22 residues processed: 150 average time/residue: 0.1615 time to fit residues: 34.9653 Evaluate side-chains 150 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 239 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.137040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.103187 restraints weight = 15997.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.107326 restraints weight = 8719.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.109828 restraints weight = 6296.440| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7839 Z= 0.256 Angle : 0.738 12.560 10619 Z= 0.372 Chirality : 0.045 0.238 1158 Planarity : 0.004 0.055 1396 Dihedral : 4.191 16.285 1055 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.99 % Allowed : 24.19 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.27), residues: 967 helix: 0.47 (0.23), residues: 480 sheet: -0.05 (0.48), residues: 123 loop : -0.35 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP C 311 HIS 0.013 0.001 HIS B 227 PHE 0.026 0.002 PHE B 270 TYR 0.034 0.002 TYR A 24 ARG 0.005 0.000 ARG B 2 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1758.37 seconds wall clock time: 33 minutes 11.97 seconds (1991.97 seconds total)