Starting phenix.real_space_refine on Wed Mar 12 22:10:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffn_31569/03_2025/7ffn_31569_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffn_31569/03_2025/7ffn_31569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ffn_31569/03_2025/7ffn_31569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffn_31569/03_2025/7ffn_31569.map" model { file = "/net/cci-nas-00/data/ceres_data/7ffn_31569/03_2025/7ffn_31569_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffn_31569/03_2025/7ffn_31569_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 67 5.16 5 C 5434 2.51 5 N 1470 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8589 Number of models: 1 Model: "" Number of chains: 6 Chain: "K" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "M" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "O" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.65 Number of scatterers: 8589 At special positions: 0 Unit cell: (150.48, 96.36, 176.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 67 16.00 O 1617 8.00 N 1470 7.00 C 5434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 42 " distance=2.03 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 55 " distance=1.09 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 64 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 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: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 31 sheets defined 17.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'K' and resid 113 through 123 removed outlier: 3.802A pdb=" N ARG K 117 " --> pdb=" O GLY K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG K 185 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.785A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN L 37 " --> pdb=" O MET L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 52 removed outlier: 4.141A pdb=" N LYS L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 48 No H-bonds generated for 'chain 'M' and resid 46 through 48' Processing helix chain 'M' and resid 55 through 59 removed outlier: 3.973A pdb=" N SER M 59 " --> pdb=" O PHE M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 5 Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.805A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 402 removed outlier: 3.515A pdb=" N THR N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.616A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 removed outlier: 4.118A pdb=" N VAL N 414 " --> pdb=" O PHE N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 3.502A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.572A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.582A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 415 removed outlier: 3.900A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 439 Processing sheet with id=AA1, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.658A pdb=" N ILE K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU K 132 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY K 138 " --> pdb=" O ILE K 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 141 through 143 Processing sheet with id=AA3, first strand: chain 'K' and resid 168 through 170 Processing sheet with id=AA4, first strand: chain 'K' and resid 190 through 191 removed outlier: 6.705A pdb=" N LYS K 190 " --> pdb=" O VAL K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 198 through 202 removed outlier: 8.494A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE K 214 " --> pdb=" O LEU K 253 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 229 through 230 removed outlier: 3.866A pdb=" N ALA K 239 " --> pdb=" O ILE K 230 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AA8, first strand: chain 'M' and resid 34 through 36 Processing sheet with id=AA9, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.928A pdb=" N CYS N 27 " --> pdb=" O CYS N 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 35 through 37 removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 35 through 37 removed outlier: 5.834A pdb=" N TYR N 98 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N SER N 51 " --> pdb=" O HIS N 96 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N HIS N 96 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N TYR N 53 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ASP N 94 " --> pdb=" O TYR N 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AB4, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AB5, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AB6, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.714A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.684A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AB9, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AC1, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AC2, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AC3, first strand: chain 'O' and resid 15 through 19 removed outlier: 5.369A pdb=" N ILE O 31 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR O 136 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN O 134 " --> pdb=" O PRO O 33 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS O 35 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR O 41 " --> pdb=" O THR O 126 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR O 126 " --> pdb=" O THR O 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 46 through 48 removed outlier: 3.640A pdb=" N TYR O 46 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 51 through 55 removed outlier: 3.715A pdb=" N ALA O 59 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 51 through 55 Processing sheet with id=AC7, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.889A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AC9, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AD1, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AD2, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.012A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AD4, first strand: chain 'O' and resid 364 through 369 316 hydrogen bonds defined for protein. 807 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: 2.69 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2743 1.34 - 1.46: 2134 1.46 - 1.59: 3844 1.59 - 1.71: 2 1.71 - 1.84: 88 Bond restraints: 8811 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.089 1.08e-02 8.57e+03 6.74e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.310 -0.076 1.21e-02 6.83e+03 3.90e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.89e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.065 1.22e-02 6.72e+03 2.81e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.505 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 11827 3.18 - 6.35: 142 6.35 - 9.53: 19 9.53 - 12.71: 2 12.71 - 15.88: 2 Bond angle restraints: 11992 Sorted by residual: angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.32 -15.88 1.93e+00 2.68e-01 6.77e+01 angle pdb=" CA VAL N 179 " pdb=" C VAL N 179 " pdb=" N SER N 180 " ideal model delta sigma weight residual 115.77 123.04 -7.27 1.25e+00 6.40e-01 3.39e+01 angle pdb=" N VAL N 179 " pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 109.80 117.18 -7.38 1.33e+00 5.65e-01 3.08e+01 angle pdb=" C VAL N 174 " pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 122.47 129.59 -7.12 1.50e+00 4.44e-01 2.25e+01 angle pdb=" C CYS N 22 " pdb=" N ALA N 23 " pdb=" CA ALA N 23 " ideal model delta sigma weight residual 121.54 130.32 -8.78 1.91e+00 2.74e-01 2.11e+01 ... (remaining 11987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5089 17.61 - 35.22: 174 35.22 - 52.82: 37 52.82 - 70.43: 5 70.43 - 88.04: 6 Dihedral angle restraints: 5311 sinusoidal: 2086 harmonic: 3225 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 27 " pdb=" CB CYS N 27 " ideal model delta sinusoidal sigma weight residual 93.00 173.64 -80.64 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA ILE O 369 " pdb=" C ILE O 369 " pdb=" N CYS O 370 " pdb=" CA CYS O 370 " ideal model delta harmonic sigma weight residual 180.00 -135.79 -44.21 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CB CYS M 37 " pdb=" SG CYS M 37 " pdb=" SG CYS M 55 " pdb=" CB CYS M 55 " ideal model delta sinusoidal sigma weight residual 93.00 14.07 78.93 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1081 0.072 - 0.144: 218 0.144 - 0.215: 27 0.215 - 0.287: 1 0.287 - 0.359: 2 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA ASP N 175 " pdb=" N ASP N 175 " pdb=" C ASP N 175 " pdb=" CB ASP N 175 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ASP M 57 " pdb=" N ASP M 57 " pdb=" C ASP M 57 " pdb=" CB ASP M 57 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA HIS N 156 " pdb=" N HIS N 156 " pdb=" C HIS N 156 " pdb=" CB HIS N 156 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1326 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " 0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 13 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO N 14 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 88 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO N 89 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO N 89 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 89 " 0.038 5.00e-02 4.00e+02 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 34 2.52 - 3.11: 5668 3.11 - 3.71: 12191 3.71 - 4.30: 17289 4.30 - 4.90: 29700 Nonbonded interactions: 64882 Sorted by model distance: nonbonded pdb=" OH TYR K 173 " pdb=" NE2 GLN O 439 " model vdw 1.924 3.120 nonbonded pdb=" O ASN O 442 " pdb=" ND2 ASN O 442 " model vdw 2.111 3.120 nonbonded pdb=" OH TYR N 359 " pdb=" O ALA O 401 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLU O 120 " pdb=" OH TYR O 122 " model vdw 2.276 3.040 nonbonded pdb=" O GLY O 182 " pdb=" OG1 THR O 263 " model vdw 2.312 3.040 ... (remaining 64877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.520 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.007 0.098 8811 Z= 0.498 Angle : 0.945 15.884 11992 Z= 0.520 Chirality : 0.058 0.359 1329 Planarity : 0.008 0.099 1549 Dihedral : 9.733 88.037 3197 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.28 % Rotamer: Outliers : 0.53 % Allowed : 2.76 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.19 % 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: -3.00 (0.21), residues: 1102 helix: -1.89 (0.34), residues: 134 sheet: -1.32 (0.26), residues: 347 loop : -2.48 (0.20), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP M 47 HIS 0.011 0.002 HIS N 28 PHE 0.023 0.003 PHE N 328 TYR 0.031 0.003 TYR O 308 ARG 0.010 0.001 ARG N 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 1.008 Fit side-chains REVERT: K 166 LYS cc_start: 0.6128 (tttt) cc_final: 0.5681 (pttt) REVERT: K 232 ASP cc_start: 0.1805 (p0) cc_final: 0.1476 (p0) REVERT: N 9 TYR cc_start: 0.8310 (m-80) cc_final: 0.8040 (m-80) REVERT: N 365 MET cc_start: 0.7551 (ttt) cc_final: 0.7237 (pmt) REVERT: N 398 THR cc_start: 0.8150 (m) cc_final: 0.7610 (t) REVERT: O 13 ILE cc_start: 0.9253 (mt) cc_final: 0.9043 (mm) REVERT: O 115 LEU cc_start: 0.8498 (tm) cc_final: 0.8134 (tp) REVERT: O 281 ASP cc_start: 0.7805 (t0) cc_final: 0.7575 (t0) REVERT: O 409 TRP cc_start: 0.8455 (m100) cc_final: 0.8235 (m100) REVERT: O 442 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5851 (t0) outliers start: 5 outliers final: 1 residues processed: 208 average time/residue: 1.2777 time to fit residues: 283.9235 Evaluate side-chains 110 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN K 211 ASN M 27 ASN M 30 ASN N 7 ASN N 52 GLN N 96 HIS N 159 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN O 66 GLN O 125 HIS O 130 GLN O 157 ASN O 264 ASN O 360 ASN O 386 HIS ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 442 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106299 restraints weight = 10962.598| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.64 r_work: 0.3009 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8811 Z= 0.310 Angle : 0.655 8.451 11992 Z= 0.341 Chirality : 0.047 0.162 1329 Planarity : 0.007 0.085 1549 Dihedral : 5.766 58.098 1207 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.93 % Allowed : 10.84 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.68 (0.24), residues: 1102 helix: 0.31 (0.45), residues: 134 sheet: -0.59 (0.27), residues: 349 loop : -1.80 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 202 HIS 0.008 0.001 HIS N 41 PHE 0.016 0.002 PHE N 328 TYR 0.023 0.002 TYR O 308 ARG 0.006 0.001 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.990 Fit side-chains REVERT: K 121 LYS cc_start: 0.8333 (pptt) cc_final: 0.8099 (tmmt) REVERT: K 166 LYS cc_start: 0.7563 (tttt) cc_final: 0.7275 (pttt) REVERT: K 190 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7854 (mtpt) REVERT: K 209 TYR cc_start: 0.8585 (t80) cc_final: 0.7947 (t80) REVERT: M 36 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8678 (ttt) REVERT: N 9 TYR cc_start: 0.8473 (m-80) cc_final: 0.8087 (m-80) REVERT: N 66 MET cc_start: 0.9458 (ttt) cc_final: 0.9173 (ttt) REVERT: N 88 ARG cc_start: 0.8812 (mtm110) cc_final: 0.6899 (mtt180) REVERT: N 113 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: N 173 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7288 (mm-30) REVERT: N 365 MET cc_start: 0.8504 (ttt) cc_final: 0.7467 (pmt) REVERT: N 398 THR cc_start: 0.8576 (m) cc_final: 0.8227 (p) REVERT: O 95 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7427 (p90) REVERT: O 175 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7756 (ttp-110) REVERT: O 409 TRP cc_start: 0.8612 (m100) cc_final: 0.8340 (m100) outliers start: 37 outliers final: 13 residues processed: 161 average time/residue: 1.2427 time to fit residues: 213.5880 Evaluate side-chains 129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 190 LYS Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain M residue 36 MET Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 160 LYS Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 43 optimal weight: 30.0000 chunk 97 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN K 211 ASN N 152 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 155 ASN O 157 ASN ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 439 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.145702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102370 restraints weight = 11081.143| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.60 r_work: 0.2959 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8811 Z= 0.320 Angle : 0.656 11.831 11992 Z= 0.337 Chirality : 0.047 0.232 1329 Planarity : 0.006 0.073 1549 Dihedral : 5.405 38.918 1202 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.10 % Allowed : 12.65 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % 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: -1.15 (0.25), residues: 1102 helix: 0.80 (0.47), residues: 141 sheet: -0.21 (0.27), residues: 355 loop : -1.52 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 202 HIS 0.006 0.001 HIS N 41 PHE 0.015 0.002 PHE N 328 TYR 0.023 0.002 TYR O 308 ARG 0.009 0.001 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7872 (ptp) cc_final: 0.7311 (ptt) REVERT: K 196 PRO cc_start: 0.8579 (Cg_endo) cc_final: 0.8352 (Cg_exo) REVERT: K 267 TYR cc_start: 0.8050 (t80) cc_final: 0.7502 (t80) REVERT: N 9 TYR cc_start: 0.8448 (m-80) cc_final: 0.8211 (m-80) REVERT: N 66 MET cc_start: 0.9465 (ttt) cc_final: 0.9191 (ttt) REVERT: N 88 ARG cc_start: 0.8814 (mtm110) cc_final: 0.6825 (mtt180) REVERT: N 173 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7262 (mm-30) REVERT: N 197 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7282 (tt) REVERT: N 256 HIS cc_start: 0.8003 (p90) cc_final: 0.7711 (p90) REVERT: N 313 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: N 365 MET cc_start: 0.8377 (ttt) cc_final: 0.7445 (pmt) REVERT: O 95 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7367 (p90) REVERT: O 175 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7772 (ttp-110) REVERT: O 281 ASP cc_start: 0.8555 (t70) cc_final: 0.8327 (t0) REVERT: O 345 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: O 409 TRP cc_start: 0.8582 (m100) cc_final: 0.8227 (m100) outliers start: 48 outliers final: 22 residues processed: 148 average time/residue: 1.1328 time to fit residues: 179.9704 Evaluate side-chains 134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain K residue 169 LYS Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 345 GLU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 0.0060 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 353 HIS ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106702 restraints weight = 11066.735| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.74 r_work: 0.3020 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 8811 Z= 0.152 Angle : 0.559 8.292 11992 Z= 0.288 Chirality : 0.045 0.256 1329 Planarity : 0.005 0.068 1549 Dihedral : 4.925 32.769 1202 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.40 % Allowed : 14.56 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -0.82 (0.25), residues: 1102 helix: 1.14 (0.47), residues: 142 sheet: -0.05 (0.28), residues: 349 loop : -1.28 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 330 HIS 0.004 0.001 HIS N 256 PHE 0.014 0.001 PHE K 128 TYR 0.021 0.001 TYR O 308 ARG 0.003 0.000 ARG O 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7751 (ptp) cc_final: 0.7181 (ptt) REVERT: K 151 MET cc_start: 0.8752 (mmm) cc_final: 0.8485 (mtp) REVERT: K 166 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7796 (ttmt) REVERT: K 196 PRO cc_start: 0.8516 (Cg_endo) cc_final: 0.8287 (Cg_exo) REVERT: K 267 TYR cc_start: 0.7977 (t80) cc_final: 0.7479 (t80) REVERT: K 270 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7136 (pm20) REVERT: N 9 TYR cc_start: 0.8347 (m-80) cc_final: 0.8052 (m-80) REVERT: N 42 ASP cc_start: 0.8233 (m-30) cc_final: 0.8012 (m-30) REVERT: N 66 MET cc_start: 0.9400 (ttt) cc_final: 0.9069 (ttt) REVERT: N 88 ARG cc_start: 0.8747 (mtm110) cc_final: 0.6838 (mtt180) REVERT: N 113 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8493 (mt-10) REVERT: N 120 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7893 (ttm-80) REVERT: N 173 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7069 (mm-30) REVERT: N 197 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7258 (tt) REVERT: N 365 MET cc_start: 0.8347 (ttt) cc_final: 0.7449 (pmt) REVERT: O 144 THR cc_start: 0.9131 (m) cc_final: 0.8900 (p) REVERT: O 175 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7729 (ttp-110) REVERT: O 345 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: O 409 TRP cc_start: 0.8644 (m100) cc_final: 0.8382 (m100) outliers start: 32 outliers final: 15 residues processed: 138 average time/residue: 1.3337 time to fit residues: 196.5071 Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 270 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 345 GLU Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 392 GLN O 394 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103218 restraints weight = 10986.457| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.72 r_work: 0.2945 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8811 Z= 0.255 Angle : 0.606 10.264 11992 Z= 0.312 Chirality : 0.046 0.258 1329 Planarity : 0.005 0.065 1549 Dihedral : 4.988 32.998 1202 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.61 % Allowed : 14.24 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % 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 (0.25), residues: 1102 helix: 1.42 (0.48), residues: 142 sheet: 0.08 (0.29), residues: 326 loop : -1.28 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 202 HIS 0.005 0.001 HIS N 41 PHE 0.019 0.001 PHE K 128 TYR 0.022 0.002 TYR O 308 ARG 0.005 0.000 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7630 (ptp) cc_final: 0.7104 (ptt) REVERT: K 151 MET cc_start: 0.8796 (mmm) cc_final: 0.8585 (mtp) REVERT: K 166 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7957 (ttmt) REVERT: K 196 PRO cc_start: 0.8574 (Cg_endo) cc_final: 0.8332 (Cg_exo) REVERT: K 267 TYR cc_start: 0.8225 (t80) cc_final: 0.7763 (t80) REVERT: K 270 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: N 66 MET cc_start: 0.9509 (ttp) cc_final: 0.9244 (ttt) REVERT: N 88 ARG cc_start: 0.8815 (mtm110) cc_final: 0.6977 (mtt180) REVERT: N 207 ILE cc_start: 0.8178 (mt) cc_final: 0.7870 (tp) REVERT: N 365 MET cc_start: 0.8420 (ttt) cc_final: 0.7443 (pmt) REVERT: O 18 ILE cc_start: 0.8739 (pt) cc_final: 0.8515 (pp) REVERT: O 175 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7973 (ttp-110) REVERT: O 209 SER cc_start: 0.9001 (m) cc_final: 0.8574 (p) REVERT: O 345 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: O 409 TRP cc_start: 0.8722 (m100) cc_final: 0.8478 (m100) outliers start: 34 outliers final: 24 residues processed: 131 average time/residue: 1.0863 time to fit residues: 152.7436 Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 270 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 345 GLU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 60 ASN O 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.098583 restraints weight = 10893.091| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.55 r_work: 0.2898 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 8811 Z= 0.484 Angle : 0.722 9.924 11992 Z= 0.372 Chirality : 0.051 0.211 1329 Planarity : 0.006 0.065 1549 Dihedral : 5.553 34.300 1202 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 5.10 % Allowed : 13.50 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.10 % 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: -0.83 (0.25), residues: 1102 helix: 1.13 (0.47), residues: 143 sheet: 0.05 (0.29), residues: 340 loop : -1.34 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 202 HIS 0.009 0.002 HIS N 41 PHE 0.026 0.002 PHE K 128 TYR 0.021 0.002 TYR O 51 ARG 0.008 0.001 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 110 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7818 (ptp) cc_final: 0.7481 (ptt) REVERT: K 151 MET cc_start: 0.8828 (mmm) cc_final: 0.8628 (mtp) REVERT: K 166 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7855 (ttmt) REVERT: K 267 TYR cc_start: 0.8483 (t80) cc_final: 0.8145 (t80) REVERT: K 270 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: N 66 MET cc_start: 0.9515 (ttp) cc_final: 0.9252 (ttt) REVERT: N 88 ARG cc_start: 0.8791 (mtm110) cc_final: 0.6942 (mtt180) REVERT: N 160 ASN cc_start: 0.6914 (t0) cc_final: 0.6596 (t0) REVERT: N 207 ILE cc_start: 0.8243 (mt) cc_final: 0.7882 (tp) REVERT: N 239 ASN cc_start: 0.8130 (t0) cc_final: 0.7488 (t0) REVERT: N 365 MET cc_start: 0.8539 (ttt) cc_final: 0.7433 (pmt) REVERT: O 18 ILE cc_start: 0.8820 (pt) cc_final: 0.8567 (pp) REVERT: O 95 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7246 (p90) REVERT: O 209 SER cc_start: 0.9016 (m) cc_final: 0.8610 (p) REVERT: O 345 GLU cc_start: 0.8523 (tp30) cc_final: 0.8191 (mm-30) REVERT: O 434 TYR cc_start: 0.7502 (t80) cc_final: 0.7252 (t80) outliers start: 48 outliers final: 28 residues processed: 137 average time/residue: 1.0327 time to fit residues: 152.9019 Evaluate side-chains 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 270 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 43 ASN O 130 GLN O 439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102049 restraints weight = 11069.698| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.57 r_work: 0.2944 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8811 Z= 0.213 Angle : 0.602 9.161 11992 Z= 0.309 Chirality : 0.045 0.201 1329 Planarity : 0.005 0.069 1549 Dihedral : 5.173 34.800 1202 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.98 % Allowed : 16.15 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1102 helix: 1.35 (0.47), residues: 143 sheet: 0.15 (0.29), residues: 335 loop : -1.22 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 89 HIS 0.004 0.001 HIS O 386 PHE 0.021 0.001 PHE K 128 TYR 0.020 0.001 TYR O 308 ARG 0.002 0.000 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7703 (ptp) cc_final: 0.7244 (ptt) REVERT: K 151 MET cc_start: 0.8776 (mmm) cc_final: 0.8519 (mtp) REVERT: K 156 LYS cc_start: 0.7816 (mmmm) cc_final: 0.7543 (tppt) REVERT: K 267 TYR cc_start: 0.8402 (t80) cc_final: 0.8069 (t80) REVERT: K 270 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: N 66 MET cc_start: 0.9431 (ttp) cc_final: 0.9226 (ttt) REVERT: N 88 ARG cc_start: 0.8753 (mtm110) cc_final: 0.6927 (mtt180) REVERT: N 160 ASN cc_start: 0.6824 (t0) cc_final: 0.6523 (t0) REVERT: N 197 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7193 (tt) REVERT: N 365 MET cc_start: 0.8506 (ttt) cc_final: 0.7412 (pmt) REVERT: O 18 ILE cc_start: 0.8712 (pt) cc_final: 0.8463 (pp) REVERT: O 95 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7248 (p90) REVERT: O 175 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8020 (ttp-110) REVERT: O 209 SER cc_start: 0.9013 (m) cc_final: 0.8592 (p) REVERT: O 345 GLU cc_start: 0.8363 (tp30) cc_final: 0.8129 (mm-30) REVERT: O 384 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8579 (mmtt) REVERT: O 434 TYR cc_start: 0.7378 (t80) cc_final: 0.7135 (t80) outliers start: 28 outliers final: 17 residues processed: 126 average time/residue: 1.1214 time to fit residues: 151.5505 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 270 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 186 VAL Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 384 LYS Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104347 restraints weight = 11148.677| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.69 r_work: 0.2974 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8811 Z= 0.146 Angle : 0.552 9.077 11992 Z= 0.284 Chirality : 0.044 0.172 1329 Planarity : 0.005 0.070 1549 Dihedral : 4.833 35.262 1202 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.34 % Allowed : 16.68 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1102 helix: 1.49 (0.48), residues: 143 sheet: 0.26 (0.30), residues: 327 loop : -1.12 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 326 HIS 0.004 0.001 HIS N 256 PHE 0.021 0.001 PHE K 128 TYR 0.019 0.001 TYR O 308 ARG 0.002 0.000 ARG N 407 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7717 (ptp) cc_final: 0.7287 (ptt) REVERT: K 151 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8489 (mtp) REVERT: K 196 PRO cc_start: 0.7988 (Cg_endo) cc_final: 0.7722 (Cg_exo) REVERT: K 267 TYR cc_start: 0.8363 (t80) cc_final: 0.8058 (t80) REVERT: K 270 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: N 66 MET cc_start: 0.9428 (ttp) cc_final: 0.9123 (ttt) REVERT: N 88 ARG cc_start: 0.8767 (mtm110) cc_final: 0.6940 (mtt180) REVERT: N 197 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7201 (tt) REVERT: N 365 MET cc_start: 0.8367 (ttt) cc_final: 0.7393 (pmt) REVERT: O 18 ILE cc_start: 0.8659 (pt) cc_final: 0.8431 (pp) REVERT: O 175 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.8006 (ttp-110) REVERT: O 345 GLU cc_start: 0.8297 (tp30) cc_final: 0.8090 (mm-30) outliers start: 22 outliers final: 14 residues processed: 122 average time/residue: 1.1461 time to fit residues: 149.7682 Evaluate side-chains 116 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 270 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 60 ASN O 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.100764 restraints weight = 11115.474| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.60 r_work: 0.2929 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8811 Z= 0.292 Angle : 0.620 9.206 11992 Z= 0.319 Chirality : 0.046 0.176 1329 Planarity : 0.005 0.068 1549 Dihedral : 5.078 36.099 1202 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.66 % Allowed : 17.43 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % 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: -0.53 (0.25), residues: 1102 helix: 1.58 (0.48), residues: 138 sheet: 0.21 (0.29), residues: 338 loop : -1.15 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 409 HIS 0.006 0.001 HIS N 256 PHE 0.025 0.002 PHE K 128 TYR 0.020 0.002 TYR O 308 ARG 0.004 0.000 ARG N 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7724 (ptp) cc_final: 0.7271 (ptt) REVERT: K 151 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8503 (mtp) REVERT: K 267 TYR cc_start: 0.8413 (t80) cc_final: 0.8122 (t80) REVERT: K 270 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7283 (pm20) REVERT: N 88 ARG cc_start: 0.8731 (mtm110) cc_final: 0.6914 (mtt180) REVERT: N 197 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7207 (tt) REVERT: N 365 MET cc_start: 0.8440 (ttt) cc_final: 0.7467 (pmt) REVERT: O 18 ILE cc_start: 0.8753 (pt) cc_final: 0.8517 (pp) REVERT: O 95 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7232 (p90) REVERT: O 175 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: O 345 GLU cc_start: 0.8331 (tp30) cc_final: 0.8037 (mm-30) REVERT: O 434 TYR cc_start: 0.7428 (t80) cc_final: 0.7196 (t80) outliers start: 25 outliers final: 17 residues processed: 118 average time/residue: 1.0672 time to fit residues: 135.4463 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 270 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 43 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN N 60 ASN O 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102920 restraints weight = 11110.811| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.60 r_work: 0.2964 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8811 Z= 0.185 Angle : 0.564 9.309 11992 Z= 0.290 Chirality : 0.044 0.170 1329 Planarity : 0.005 0.070 1549 Dihedral : 4.901 35.826 1202 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.23 % Allowed : 17.96 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % 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 (0.25), residues: 1102 helix: 1.64 (0.48), residues: 139 sheet: 0.22 (0.29), residues: 337 loop : -1.06 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 409 HIS 0.005 0.001 HIS N 256 PHE 0.022 0.001 PHE K 128 TYR 0.018 0.001 TYR O 308 ARG 0.002 0.000 ARG N 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7733 (ptp) cc_final: 0.7285 (ptt) REVERT: K 151 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8429 (mtp) REVERT: K 267 TYR cc_start: 0.8379 (t80) cc_final: 0.8088 (t80) REVERT: K 270 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: N 66 MET cc_start: 0.9415 (ttt) cc_final: 0.9127 (ttt) REVERT: N 88 ARG cc_start: 0.8694 (mtm110) cc_final: 0.6890 (mtt180) REVERT: N 197 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7219 (tt) REVERT: N 365 MET cc_start: 0.8423 (ttt) cc_final: 0.7466 (pmt) REVERT: O 18 ILE cc_start: 0.8695 (pt) cc_final: 0.8451 (pp) REVERT: O 175 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.7931 (ttp-110) REVERT: O 345 GLU cc_start: 0.8254 (tp30) cc_final: 0.8051 (mm-30) REVERT: O 434 TYR cc_start: 0.7305 (t80) cc_final: 0.7082 (t80) outliers start: 21 outliers final: 16 residues processed: 122 average time/residue: 1.1219 time to fit residues: 147.3538 Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain K residue 270 GLU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN K 211 ASN N 60 ASN O 130 GLN O 439 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107009 restraints weight = 11140.302| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.74 r_work: 0.2821 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8811 Z= 0.376 Angle : 0.660 9.689 11992 Z= 0.340 Chirality : 0.048 0.185 1329 Planarity : 0.005 0.068 1549 Dihedral : 5.269 36.548 1202 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.44 % Allowed : 17.75 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.10 % 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 (0.25), residues: 1102 helix: 1.57 (0.48), residues: 138 sheet: 0.17 (0.29), residues: 341 loop : -1.14 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 409 HIS 0.006 0.001 HIS N 41 PHE 0.028 0.002 PHE K 128 TYR 0.020 0.002 TYR O 308 ARG 0.006 0.001 ARG N 298 =============================================================================== Job complete usr+sys time: 8529.37 seconds wall clock time: 148 minutes 24.41 seconds (8904.41 seconds total)