Starting phenix.real_space_refine on Fri Dec 27 20:48:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rp6_24613/12_2024/7rp6_24613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rp6_24613/12_2024/7rp6_24613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rp6_24613/12_2024/7rp6_24613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rp6_24613/12_2024/7rp6_24613.map" model { file = "/net/cci-nas-00/data/ceres_data/7rp6_24613/12_2024/7rp6_24613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rp6_24613/12_2024/7rp6_24613.cif" } resolution = 3.78 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= 0.003 sd= 0.036 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 40 5.16 5 C 4435 2.51 5 N 1138 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6753 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3374 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 430} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Time building chain proxies: 4.77, per 1000 atoms: 0.71 Number of scatterers: 6753 At special positions: 0 Unit cell: (77.552, 76.504, 114.232, 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 40 16.00 O 1140 8.00 N 1138 7.00 C 4435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 347 " distance=2.78 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.696A pdb=" N ARG A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 71 removed outlier: 4.253A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 42 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 4.116A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.839A pdb=" N GLY A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.714A pdb=" N ALA A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.788A pdb=" N LEU A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 5.373A pdb=" N PHE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.593A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 188 removed outlier: 4.256A pdb=" N LEU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 214 through 231 removed outlier: 3.635A pdb=" N VAL A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 283 removed outlier: 3.948A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.704A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 308 removed outlier: 3.851A pdb=" N CYS A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 329 through 349 removed outlier: 4.194A pdb=" N PHE A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 379 removed outlier: 3.705A pdb=" N LEU A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.442A pdb=" N PHE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 406 through 415 removed outlier: 4.240A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.786A pdb=" N LEU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 4.055A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 removed outlier: 3.776A pdb=" N ARG B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 67 removed outlier: 4.526A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 42 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 74 through 101 removed outlier: 4.069A pdb=" N VAL B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 105 removed outlier: 3.538A pdb=" N GLY B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 123 through 141 removed outlier: 3.755A pdb=" N LEU B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) Proline residue: B 129 - end of helix removed outlier: 5.025A pdb=" N PHE B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 removed outlier: 3.651A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 188 removed outlier: 4.266A pdb=" N LEU B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 214 through 232 removed outlier: 4.098A pdb=" N MET B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 251 through 283 removed outlier: 3.876A pdb=" N TYR B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 3.887A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 removed outlier: 3.582A pdb=" N CYS B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.643A pdb=" N THR B 312 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 313 " --> pdb=" O PRO B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 313' Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.587A pdb=" N ALA B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 348 removed outlier: 3.939A pdb=" N PHE B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 357 through 379 removed outlier: 4.062A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 Processing helix chain 'B' and resid 386 through 395 removed outlier: 4.166A pdb=" N ALA B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 406 through 415 removed outlier: 4.029A pdb=" N VAL B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.597A pdb=" N THR B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 459 removed outlier: 4.136A pdb=" N LEU B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1236 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: 1.84 Time building geometry restraints manager: 2.09 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: 2131 1.34 - 1.46: 1433 1.46 - 1.58: 3258 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 6896 Sorted by residual: bond pdb=" N CYS B 302 " pdb=" CA CYS B 302 " ideal model delta sigma weight residual 1.459 1.485 -0.027 1.25e-02 6.40e+03 4.53e+00 bond pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.20e-02 6.94e+03 3.60e+00 bond pdb=" C LEU B 128 " pdb=" N PRO B 129 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" N ASN B 233 " pdb=" CA ASN B 233 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.42e-02 4.96e+03 3.38e+00 bond pdb=" C LEU A 128 " pdb=" N PRO A 129 " ideal model delta sigma weight residual 1.334 1.376 -0.043 2.34e-02 1.83e+03 3.31e+00 ... (remaining 6891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 9061 2.40 - 4.80: 246 4.80 - 7.20: 35 7.20 - 9.59: 14 9.59 - 11.99: 2 Bond angle restraints: 9358 Sorted by residual: angle pdb=" C PHE A 232 " pdb=" N ASN A 233 " pdb=" CA ASN A 233 " ideal model delta sigma weight residual 122.77 115.61 7.16 1.33e+00 5.65e-01 2.90e+01 angle pdb=" CA ILE B 320 " pdb=" C ILE B 320 " pdb=" N PRO B 321 " ideal model delta sigma weight residual 120.83 124.06 -3.23 6.10e-01 2.69e+00 2.80e+01 angle pdb=" N LEU B 301 " pdb=" CA LEU B 301 " pdb=" C LEU B 301 " ideal model delta sigma weight residual 111.14 106.08 5.06 1.08e+00 8.57e-01 2.19e+01 angle pdb=" C PHE B 166 " pdb=" N ARG B 167 " pdb=" CA ARG B 167 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C ASN B 233 " pdb=" N HIS B 234 " pdb=" CA HIS B 234 " ideal model delta sigma weight residual 121.19 127.74 -6.55 1.59e+00 3.96e-01 1.70e+01 ... (remaining 9353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 3503 17.08 - 34.16: 409 34.16 - 51.23: 84 51.23 - 68.31: 9 68.31 - 85.39: 8 Dihedral angle restraints: 4013 sinusoidal: 1525 harmonic: 2488 Sorted by residual: dihedral pdb=" CB CYS B 302 " pdb=" SG CYS B 302 " pdb=" SG CYS B 347 " pdb=" CB CYS B 347 " ideal model delta sinusoidal sigma weight residual 93.00 177.18 -84.18 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CA VAL B 162 " pdb=" C VAL B 162 " pdb=" N LEU B 163 " pdb=" CA LEU B 163 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA VAL A 162 " pdb=" C VAL A 162 " pdb=" N LEU A 163 " pdb=" CA LEU A 163 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 4010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 957 0.079 - 0.159: 133 0.159 - 0.238: 8 0.238 - 0.318: 3 0.318 - 0.397: 1 Chirality restraints: 1102 Sorted by residual: chirality pdb=" CB ILE B 356 " pdb=" CA ILE B 356 " pdb=" CG1 ILE B 356 " pdb=" CG2 ILE B 356 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE B 320 " pdb=" CA ILE B 320 " pdb=" CG1 ILE B 320 " pdb=" CG2 ILE B 320 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1099 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 300 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C GLY B 300 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY B 300 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU B 301 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 205 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO A 206 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 149 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO A 150 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.035 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2284 2.85 - 3.36: 6543 3.36 - 3.87: 11297 3.87 - 4.39: 12540 4.39 - 4.90: 21838 Nonbonded interactions: 54502 Sorted by model distance: nonbonded pdb=" O SER B 350 " pdb=" OG SER B 350 " model vdw 2.334 3.040 nonbonded pdb=" OD1 ASN B 287 " pdb=" OG1 THR B 289 " model vdw 2.373 3.040 nonbonded pdb=" NZ LYS B 131 " pdb=" OE1 GLN B 153 " model vdw 2.378 3.120 nonbonded pdb=" NZ LYS A 131 " pdb=" OE1 GLN A 153 " model vdw 2.379 3.120 nonbonded pdb=" OD1 ASP A 278 " pdb=" NH1 ARG A 451 " model vdw 2.396 3.120 ... (remaining 54497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 12 through 233 or (resid 234 and (name N or name CA or nam \ e C or name O or name CB )) or resid 235 through 461)) } 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: 1.330 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.790 Find NCS groups from input model: 0.210 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.006 0.066 6896 Z= 0.373 Angle : 0.956 11.992 9358 Z= 0.516 Chirality : 0.058 0.397 1102 Planarity : 0.008 0.072 1175 Dihedral : 14.846 85.390 2438 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.59 % Allowed : 9.60 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.21), residues: 896 helix: -2.99 (0.14), residues: 666 sheet: None (None), residues: 0 loop : -2.79 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 124 HIS 0.003 0.001 HIS B 284 PHE 0.028 0.002 PHE A 219 TYR 0.012 0.002 TYR B 229 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8375 (t80) cc_final: 0.7952 (t80) REVERT: A 132 PHE cc_start: 0.8059 (t80) cc_final: 0.7834 (t80) REVERT: A 210 TYR cc_start: 0.8289 (t80) cc_final: 0.7947 (t80) REVERT: A 228 MET cc_start: 0.8354 (tpp) cc_final: 0.7833 (mmt) REVERT: A 253 TRP cc_start: 0.8076 (p-90) cc_final: 0.7599 (p-90) REVERT: A 318 ASN cc_start: 0.7609 (p0) cc_final: 0.7392 (p0) REVERT: A 459 GLU cc_start: 0.7254 (mp0) cc_final: 0.6794 (mp0) REVERT: B 16 LEU cc_start: 0.8706 (pp) cc_final: 0.8418 (pp) REVERT: B 100 TYR cc_start: 0.8152 (m-80) cc_final: 0.7716 (m-80) REVERT: B 228 MET cc_start: 0.7670 (mmm) cc_final: 0.7310 (mmm) REVERT: B 264 ILE cc_start: 0.8808 (tt) cc_final: 0.8582 (tt) REVERT: B 335 PHE cc_start: 0.8690 (t80) cc_final: 0.8418 (t80) REVERT: B 342 ILE cc_start: 0.8844 (mm) cc_final: 0.8626 (tp) REVERT: B 421 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7957 (pp) outliers start: 4 outliers final: 1 residues processed: 194 average time/residue: 0.1775 time to fit residues: 46.6881 Evaluate side-chains 145 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.0670 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN B 70 HIS B 74 ASN B 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6896 Z= 0.195 Angle : 0.628 9.253 9358 Z= 0.312 Chirality : 0.041 0.154 1102 Planarity : 0.005 0.057 1175 Dihedral : 5.374 29.903 964 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.69 % Allowed : 15.66 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.26), residues: 896 helix: -1.46 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -2.37 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 291 HIS 0.006 0.001 HIS B 284 PHE 0.023 0.001 PHE B 92 TYR 0.007 0.001 TYR A 100 ARG 0.007 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8401 (t80) cc_final: 0.8095 (t80) REVERT: A 132 PHE cc_start: 0.8095 (t80) cc_final: 0.7771 (t80) REVERT: A 210 TYR cc_start: 0.8234 (t80) cc_final: 0.7946 (t80) REVERT: A 228 MET cc_start: 0.8441 (tpp) cc_final: 0.7839 (mmt) REVERT: A 253 TRP cc_start: 0.8013 (p-90) cc_final: 0.7531 (p-90) REVERT: A 318 ASN cc_start: 0.7680 (p0) cc_final: 0.7471 (p0) REVERT: A 421 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8129 (pp) REVERT: A 459 GLU cc_start: 0.7317 (mp0) cc_final: 0.6826 (mp0) REVERT: B 100 TYR cc_start: 0.8151 (m-80) cc_final: 0.7762 (m-80) REVERT: B 228 MET cc_start: 0.7603 (mmm) cc_final: 0.7399 (mmm) REVERT: B 284 HIS cc_start: 0.8086 (p-80) cc_final: 0.7814 (p90) REVERT: B 335 PHE cc_start: 0.8713 (t80) cc_final: 0.8462 (t80) REVERT: B 421 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7875 (pp) outliers start: 25 outliers final: 14 residues processed: 186 average time/residue: 0.1594 time to fit residues: 42.0051 Evaluate side-chains 165 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN B 63 GLN ** B 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6896 Z= 0.189 Angle : 0.611 9.035 9358 Z= 0.304 Chirality : 0.042 0.158 1102 Planarity : 0.004 0.051 1175 Dihedral : 4.996 29.274 962 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.28 % Allowed : 19.79 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.28), residues: 896 helix: -0.76 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 291 HIS 0.006 0.001 HIS B 284 PHE 0.012 0.001 PHE A 219 TYR 0.007 0.001 TYR B 100 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8450 (t80) cc_final: 0.8143 (t80) REVERT: A 132 PHE cc_start: 0.8115 (t80) cc_final: 0.7815 (t80) REVERT: A 210 TYR cc_start: 0.8212 (t80) cc_final: 0.7947 (t80) REVERT: A 228 MET cc_start: 0.8461 (tpp) cc_final: 0.7817 (mmt) REVERT: A 253 TRP cc_start: 0.8007 (p-90) cc_final: 0.7525 (p-90) REVERT: A 318 ASN cc_start: 0.7706 (p0) cc_final: 0.7489 (p0) REVERT: A 421 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8166 (pp) REVERT: A 438 PHE cc_start: 0.7523 (m-10) cc_final: 0.6949 (t80) REVERT: A 459 GLU cc_start: 0.7414 (mp0) cc_final: 0.6895 (mp0) REVERT: B 100 TYR cc_start: 0.8145 (m-80) cc_final: 0.7699 (m-80) REVERT: B 228 MET cc_start: 0.7663 (mmm) cc_final: 0.7345 (mmm) REVERT: B 280 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 335 PHE cc_start: 0.8720 (t80) cc_final: 0.8400 (t80) REVERT: B 421 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7861 (pp) outliers start: 29 outliers final: 15 residues processed: 172 average time/residue: 0.1505 time to fit residues: 37.1647 Evaluate side-chains 166 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.0270 chunk 54 optimal weight: 0.0770 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN B 20 GLN B 63 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6896 Z= 0.201 Angle : 0.604 9.581 9358 Z= 0.301 Chirality : 0.042 0.140 1102 Planarity : 0.005 0.047 1175 Dihedral : 4.871 28.867 962 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.28 % Allowed : 22.16 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.29), residues: 896 helix: -0.36 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -1.75 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 59 HIS 0.003 0.001 HIS B 284 PHE 0.012 0.001 PHE A 83 TYR 0.009 0.001 TYR B 100 ARG 0.005 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.748 Fit side-chains REVERT: A 92 PHE cc_start: 0.8417 (t80) cc_final: 0.8159 (t80) REVERT: A 98 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8285 (tpp80) REVERT: A 210 TYR cc_start: 0.8228 (t80) cc_final: 0.7975 (t80) REVERT: A 253 TRP cc_start: 0.8064 (p-90) cc_final: 0.7578 (p-90) REVERT: A 318 ASN cc_start: 0.7737 (p0) cc_final: 0.7521 (p0) REVERT: A 421 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8172 (pp) REVERT: A 438 PHE cc_start: 0.7499 (m-10) cc_final: 0.6948 (t80) REVERT: A 459 GLU cc_start: 0.7460 (mp0) cc_final: 0.7079 (mp0) REVERT: B 20 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: B 100 TYR cc_start: 0.8117 (m-80) cc_final: 0.7648 (m-80) REVERT: B 335 PHE cc_start: 0.8705 (t80) cc_final: 0.8426 (t80) REVERT: B 421 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7900 (pp) outliers start: 29 outliers final: 20 residues processed: 170 average time/residue: 0.1406 time to fit residues: 34.8032 Evaluate side-chains 172 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN B 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6896 Z= 0.246 Angle : 0.631 9.961 9358 Z= 0.313 Chirality : 0.043 0.150 1102 Planarity : 0.004 0.047 1175 Dihedral : 4.836 28.583 962 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.32 % Allowed : 22.60 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.29), residues: 896 helix: -0.25 (0.21), residues: 672 sheet: None (None), residues: 0 loop : -1.64 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 59 HIS 0.003 0.001 HIS B 284 PHE 0.013 0.001 PHE A 348 TYR 0.009 0.001 TYR B 419 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8433 (t80) cc_final: 0.8183 (t80) REVERT: A 98 ARG cc_start: 0.8679 (tpp-160) cc_final: 0.8387 (tpp80) REVERT: A 210 TYR cc_start: 0.8238 (t80) cc_final: 0.7982 (t80) REVERT: A 253 TRP cc_start: 0.8124 (p-90) cc_final: 0.7650 (p-90) REVERT: A 421 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8177 (pp) REVERT: A 438 PHE cc_start: 0.7551 (m-10) cc_final: 0.7007 (t80) REVERT: A 459 GLU cc_start: 0.7465 (mp0) cc_final: 0.7060 (mp0) REVERT: B 100 TYR cc_start: 0.8156 (m-80) cc_final: 0.7719 (m-80) REVERT: B 335 PHE cc_start: 0.8692 (t80) cc_final: 0.8419 (t80) REVERT: B 421 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7873 (pp) outliers start: 36 outliers final: 24 residues processed: 168 average time/residue: 0.1315 time to fit residues: 32.3858 Evaluate side-chains 170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 83 optimal weight: 0.0370 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6896 Z= 0.172 Angle : 0.605 10.179 9358 Z= 0.300 Chirality : 0.042 0.130 1102 Planarity : 0.004 0.045 1175 Dihedral : 4.746 29.277 962 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.28 % Allowed : 23.04 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.29), residues: 896 helix: -0.04 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -1.53 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 59 HIS 0.003 0.001 HIS B 284 PHE 0.019 0.001 PHE B 92 TYR 0.009 0.001 TYR B 419 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8281 (t80) cc_final: 0.8034 (t80) REVERT: A 98 ARG cc_start: 0.8699 (tpp-160) cc_final: 0.8425 (tpp80) REVERT: A 210 TYR cc_start: 0.8265 (t80) cc_final: 0.8028 (t80) REVERT: A 228 MET cc_start: 0.8388 (tpp) cc_final: 0.8147 (mmm) REVERT: A 253 TRP cc_start: 0.8067 (p-90) cc_final: 0.7563 (p-90) REVERT: A 421 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8223 (pp) REVERT: A 438 PHE cc_start: 0.7444 (m-10) cc_final: 0.6950 (t80) REVERT: A 459 GLU cc_start: 0.7437 (mp0) cc_final: 0.7111 (mp0) REVERT: B 100 TYR cc_start: 0.8118 (m-80) cc_final: 0.7638 (m-80) REVERT: B 228 MET cc_start: 0.7560 (mmm) cc_final: 0.7263 (mmm) REVERT: B 264 ILE cc_start: 0.8889 (tt) cc_final: 0.8676 (pt) REVERT: B 335 PHE cc_start: 0.8666 (t80) cc_final: 0.8373 (t80) REVERT: B 421 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7788 (pp) outliers start: 29 outliers final: 18 residues processed: 169 average time/residue: 0.1503 time to fit residues: 36.9955 Evaluate side-chains 162 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 0.0010 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6896 Z= 0.190 Angle : 0.609 10.536 9358 Z= 0.301 Chirality : 0.042 0.138 1102 Planarity : 0.004 0.045 1175 Dihedral : 4.700 28.844 962 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.14 % Allowed : 24.22 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 896 helix: 0.16 (0.21), residues: 664 sheet: None (None), residues: 0 loop : -1.64 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 59 HIS 0.005 0.001 HIS B 284 PHE 0.009 0.001 PHE A 348 TYR 0.008 0.001 TYR B 419 ARG 0.007 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8272 (t80) cc_final: 0.8010 (t80) REVERT: A 98 ARG cc_start: 0.8689 (tpp-160) cc_final: 0.8479 (tpp80) REVERT: A 210 TYR cc_start: 0.8260 (t80) cc_final: 0.8024 (t80) REVERT: A 253 TRP cc_start: 0.8080 (p-90) cc_final: 0.7572 (p-90) REVERT: A 409 ILE cc_start: 0.9440 (mm) cc_final: 0.9234 (mp) REVERT: A 421 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8247 (pp) REVERT: A 438 PHE cc_start: 0.7414 (m-10) cc_final: 0.6925 (t80) REVERT: A 459 GLU cc_start: 0.7439 (mp0) cc_final: 0.7130 (mp0) REVERT: B 100 TYR cc_start: 0.8128 (m-80) cc_final: 0.7668 (m-80) REVERT: B 228 MET cc_start: 0.7563 (mmm) cc_final: 0.7320 (mmm) REVERT: B 264 ILE cc_start: 0.8886 (tt) cc_final: 0.8669 (pt) REVERT: B 335 PHE cc_start: 0.8686 (t80) cc_final: 0.8368 (t80) REVERT: B 378 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7824 (tt) REVERT: B 421 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7858 (pp) outliers start: 28 outliers final: 21 residues processed: 156 average time/residue: 0.1354 time to fit residues: 31.0386 Evaluate side-chains 165 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6896 Z= 0.212 Angle : 0.621 10.450 9358 Z= 0.306 Chirality : 0.043 0.173 1102 Planarity : 0.004 0.045 1175 Dihedral : 4.695 28.614 962 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.73 % Allowed : 24.37 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.29), residues: 896 helix: 0.23 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -1.53 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 59 HIS 0.004 0.001 HIS B 284 PHE 0.038 0.001 PHE B 379 TYR 0.008 0.001 TYR B 419 ARG 0.007 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8293 (t80) cc_final: 0.8046 (t80) REVERT: A 210 TYR cc_start: 0.8262 (t80) cc_final: 0.8026 (t80) REVERT: A 253 TRP cc_start: 0.8106 (p-90) cc_final: 0.7594 (p-90) REVERT: A 421 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8245 (pp) REVERT: A 438 PHE cc_start: 0.7398 (m-10) cc_final: 0.6905 (t80) REVERT: A 459 GLU cc_start: 0.7399 (mp0) cc_final: 0.7133 (mp0) REVERT: B 20 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 100 TYR cc_start: 0.8145 (m-80) cc_final: 0.7688 (m-80) REVERT: B 128 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8429 (tt) REVERT: B 228 MET cc_start: 0.7587 (mmm) cc_final: 0.7288 (mmm) REVERT: B 264 ILE cc_start: 0.8881 (tt) cc_final: 0.8666 (pt) REVERT: B 335 PHE cc_start: 0.8706 (t80) cc_final: 0.8400 (t80) REVERT: B 421 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7872 (pp) outliers start: 32 outliers final: 26 residues processed: 159 average time/residue: 0.1440 time to fit residues: 34.4124 Evaluate side-chains 169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6896 Z= 0.198 Angle : 0.625 10.648 9358 Z= 0.308 Chirality : 0.042 0.152 1102 Planarity : 0.004 0.046 1175 Dihedral : 4.707 28.606 962 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.43 % Allowed : 24.67 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.29), residues: 896 helix: 0.32 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -1.50 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 59 HIS 0.004 0.001 HIS B 284 PHE 0.009 0.001 PHE A 348 TYR 0.008 0.001 TYR B 419 ARG 0.007 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8277 (t80) cc_final: 0.7998 (t80) REVERT: A 210 TYR cc_start: 0.8260 (t80) cc_final: 0.8027 (t80) REVERT: A 253 TRP cc_start: 0.8104 (p-90) cc_final: 0.7596 (p-90) REVERT: A 421 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8232 (pp) REVERT: A 438 PHE cc_start: 0.7284 (m-10) cc_final: 0.6884 (t80) REVERT: A 459 GLU cc_start: 0.7391 (mp0) cc_final: 0.7119 (mp0) REVERT: B 20 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 100 TYR cc_start: 0.8138 (m-80) cc_final: 0.7701 (m-80) REVERT: B 224 MET cc_start: 0.7457 (mmm) cc_final: 0.7148 (mmt) REVERT: B 228 MET cc_start: 0.7621 (mmm) cc_final: 0.7306 (mmm) REVERT: B 264 ILE cc_start: 0.8885 (tt) cc_final: 0.8679 (pt) REVERT: B 335 PHE cc_start: 0.8728 (t80) cc_final: 0.8402 (t80) REVERT: B 421 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7808 (pp) outliers start: 30 outliers final: 25 residues processed: 155 average time/residue: 0.1345 time to fit residues: 31.0194 Evaluate side-chains 165 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6896 Z= 0.221 Angle : 0.632 10.634 9358 Z= 0.311 Chirality : 0.042 0.147 1102 Planarity : 0.004 0.045 1175 Dihedral : 4.709 28.299 962 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.43 % Allowed : 25.11 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 896 helix: 0.36 (0.21), residues: 666 sheet: None (None), residues: 0 loop : -1.48 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 59 HIS 0.004 0.001 HIS B 284 PHE 0.025 0.001 PHE B 92 TYR 0.008 0.001 TYR B 100 ARG 0.007 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8293 (t80) cc_final: 0.8018 (t80) REVERT: A 210 TYR cc_start: 0.8266 (t80) cc_final: 0.8031 (t80) REVERT: A 253 TRP cc_start: 0.8122 (p-90) cc_final: 0.7610 (p-90) REVERT: A 421 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8256 (pp) REVERT: A 438 PHE cc_start: 0.7243 (m-10) cc_final: 0.6852 (t80) REVERT: A 459 GLU cc_start: 0.7398 (mp0) cc_final: 0.7159 (mp0) REVERT: B 20 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 100 TYR cc_start: 0.8152 (m-80) cc_final: 0.7719 (m-80) REVERT: B 128 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8422 (tt) REVERT: B 335 PHE cc_start: 0.8718 (t80) cc_final: 0.8394 (t80) REVERT: B 421 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7864 (pp) outliers start: 30 outliers final: 25 residues processed: 156 average time/residue: 0.1215 time to fit residues: 28.5437 Evaluate side-chains 167 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 MET Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN B 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.112373 restraints weight = 9488.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.115622 restraints weight = 5788.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.117819 restraints weight = 4246.574| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6896 Z= 0.210 Angle : 0.633 10.701 9358 Z= 0.311 Chirality : 0.043 0.142 1102 Planarity : 0.004 0.046 1175 Dihedral : 4.706 28.475 962 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.58 % Allowed : 25.41 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.29), residues: 896 helix: 0.38 (0.21), residues: 668 sheet: None (None), residues: 0 loop : -1.41 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 59 HIS 0.004 0.001 HIS B 284 PHE 0.010 0.001 PHE A 348 TYR 0.007 0.001 TYR B 100 ARG 0.007 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1586.20 seconds wall clock time: 29 minutes 54.24 seconds (1794.24 seconds total)