Starting phenix.real_space_refine on Sat Jul 26 04:32:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffn_31569/07_2025/7ffn_31569_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffn_31569/07_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_31569/07_2025/7ffn_31569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffn_31569/07_2025/7ffn_31569.map" model { file = "/net/cci-nas-00/data/ceres_data/7ffn_31569/07_2025/7ffn_31569_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffn_31569/07_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-5711/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: 5.36, per 1000 atoms: 0.62 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: 2.09 Conformation dependent library (CDL) restraints added in 990.4 milliseconds 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: 1.55 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: 2.70 Time building geometry restraints manager: 2.49 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.900 ------------------------------------------------------------------------------- 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 : 0.012 0.938 8827 Z= 0.601 Angle : 1.008 26.552 12024 Z= 0.546 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 Details of bonding type rmsd hydrogen bonds : bond 0.21044 ( 298) hydrogen bonds : angle 8.76345 ( 807) SS BOND : bond 0.23452 ( 16) SS BOND : angle 6.85804 ( 32) covalent geometry : bond 0.00745 ( 8811) covalent geometry : angle 0.94538 (11992) *********************** 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 : 1.024 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: 1.2750 time to fit residues: 283.3803 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 : 1.096 ------------------------------------------------------------------------------- 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: 4.9990 chunk 82 optimal weight: 6.9990 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: 4.1990 ------------------------------------------------------------------------------- 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 3 HIS O 66 GLN O 125 HIS O 157 ASN O 264 ASN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104807 restraints weight = 10952.538| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.65 r_work: 0.2986 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8827 Z= 0.222 Angle : 0.688 8.586 12024 Z= 0.356 Chirality : 0.047 0.166 1329 Planarity : 0.007 0.082 1549 Dihedral : 5.885 59.374 1207 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.25 % Allowed : 10.73 % Favored : 85.02 % 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: -1.72 (0.24), residues: 1102 helix: 0.20 (0.44), residues: 138 sheet: -0.55 (0.27), residues: 348 loop : -1.86 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 202 HIS 0.008 0.002 HIS N 41 PHE 0.018 0.002 PHE N 328 TYR 0.023 0.002 TYR O 308 ARG 0.006 0.001 ARG O 267 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 298) hydrogen bonds : angle 5.54808 ( 807) SS BOND : bond 0.00472 ( 16) SS BOND : angle 1.82211 ( 32) covalent geometry : bond 0.00544 ( 8811) covalent geometry : angle 0.68234 (11992) *********************** 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 183 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 1.197 Fit side-chains REVERT: K 121 LYS cc_start: 0.8329 (pptt) cc_final: 0.8094 (tmmt) REVERT: K 166 LYS cc_start: 0.7591 (tttt) cc_final: 0.7293 (pttt) REVERT: K 209 TYR cc_start: 0.8602 (t80) cc_final: 0.8045 (t80) REVERT: K 267 TYR cc_start: 0.7703 (t80) cc_final: 0.7336 (t80) REVERT: N 66 MET cc_start: 0.9463 (ttt) cc_final: 0.9165 (ttt) REVERT: N 88 ARG cc_start: 0.8838 (mtm110) cc_final: 0.6916 (mtt180) REVERT: N 113 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: N 173 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7297 (mm-30) REVERT: N 365 MET cc_start: 0.8526 (ttt) cc_final: 0.7552 (pmt) REVERT: N 398 THR cc_start: 0.8576 (m) cc_final: 0.8214 (p) REVERT: O 24 TYR cc_start: 0.8735 (m-80) cc_final: 0.8534 (m-80) REVERT: O 95 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7435 (p90) REVERT: O 100 ASN cc_start: 0.8628 (m-40) cc_final: 0.8077 (m-40) REVERT: O 175 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7781 (ttp-110) REVERT: O 409 TRP cc_start: 0.8621 (m100) cc_final: 0.8338 (m100) outliers start: 40 outliers final: 14 residues processed: 166 average time/residue: 1.3522 time to fit residues: 239.5137 Evaluate side-chains 131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 242 LEU 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 277 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: 5.9990 chunk 103 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 24 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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** N 353 HIS O 130 GLN O 155 ASN O 157 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104627 restraints weight = 11099.860| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.60 r_work: 0.2987 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8827 Z= 0.147 Angle : 0.615 9.611 12024 Z= 0.317 Chirality : 0.045 0.258 1329 Planarity : 0.006 0.076 1549 Dihedral : 5.277 39.505 1202 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.72 % Allowed : 12.96 % Favored : 83.32 % 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: -1.14 (0.25), residues: 1102 helix: 0.78 (0.47), residues: 141 sheet: -0.27 (0.27), residues: 352 loop : -1.46 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 202 HIS 0.004 0.001 HIS O 386 PHE 0.013 0.001 PHE N 328 TYR 0.021 0.002 TYR O 308 ARG 0.005 0.000 ARG N 298 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 298) hydrogen bonds : angle 5.07931 ( 807) SS BOND : bond 0.00467 ( 16) SS BOND : angle 1.80473 ( 32) covalent geometry : bond 0.00358 ( 8811) covalent geometry : angle 0.60908 (11992) *********************** 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 156 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7830 (ptp) cc_final: 0.7435 (ptt) REVERT: K 196 PRO cc_start: 0.8523 (Cg_endo) cc_final: 0.8314 (Cg_exo) REVERT: K 267 TYR cc_start: 0.7975 (t80) cc_final: 0.7472 (t80) REVERT: K 270 GLU cc_start: 0.6642 (pm20) cc_final: 0.6348 (pm20) REVERT: N 9 TYR cc_start: 0.8448 (m-80) cc_final: 0.8139 (m-80) REVERT: N 66 MET cc_start: 0.9412 (ttt) cc_final: 0.9045 (ttt) REVERT: N 88 ARG cc_start: 0.8788 (mtm110) cc_final: 0.6838 (mtt180) REVERT: N 173 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7278 (mm-30) REVERT: N 197 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7235 (tt) REVERT: N 365 MET cc_start: 0.8368 (ttt) cc_final: 0.7427 (pmt) REVERT: O 24 TYR cc_start: 0.8779 (m-80) cc_final: 0.8565 (m-80) REVERT: O 175 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7701 (ttp-110) REVERT: O 281 ASP cc_start: 0.8608 (t70) cc_final: 0.8391 (t0) REVERT: O 345 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: O 409 TRP cc_start: 0.8557 (m100) cc_final: 0.8231 (m100) outliers start: 35 outliers final: 17 residues processed: 142 average time/residue: 1.0541 time to fit residues: 160.8051 Evaluate side-chains 127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 282 SER Chi-restraints excluded: chain N residue 394 VAL 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 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: 4.9990 chunk 47 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3684 r_free = 0.3684 target = 0.146759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104294 restraints weight = 10987.464| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.61 r_work: 0.2974 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8827 Z= 0.148 Angle : 0.605 8.561 12024 Z= 0.312 Chirality : 0.046 0.231 1329 Planarity : 0.005 0.068 1549 Dihedral : 5.070 33.456 1202 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.93 % Allowed : 13.60 % Favored : 82.47 % 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: 1.19 (0.47), residues: 141 sheet: -0.02 (0.27), residues: 359 loop : -1.33 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 339 HIS 0.004 0.001 HIS N 41 PHE 0.014 0.001 PHE K 128 TYR 0.021 0.002 TYR O 308 ARG 0.003 0.000 ARG N 298 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 298) hydrogen bonds : angle 4.85512 ( 807) SS BOND : bond 0.00448 ( 16) SS BOND : angle 2.20850 ( 32) covalent geometry : bond 0.00363 ( 8811) covalent geometry : angle 0.59461 (11992) *********************** 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 152 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7584 (ptp) cc_final: 0.6923 (ptt) REVERT: K 121 LYS cc_start: 0.8270 (pptt) cc_final: 0.8044 (tmmt) REVERT: K 196 PRO cc_start: 0.8553 (Cg_endo) cc_final: 0.8319 (Cg_exo) REVERT: K 267 TYR cc_start: 0.8189 (t80) cc_final: 0.7681 (t80) REVERT: K 270 GLU cc_start: 0.6539 (pm20) cc_final: 0.6315 (pm20) REVERT: N 9 TYR cc_start: 0.8377 (m-80) cc_final: 0.8090 (m-80) REVERT: N 66 MET cc_start: 0.9420 (ttt) cc_final: 0.9039 (ttt) REVERT: N 88 ARG cc_start: 0.8805 (mtm110) cc_final: 0.7013 (mtt180) REVERT: N 173 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7206 (mm-30) REVERT: N 207 ILE cc_start: 0.8193 (mt) cc_final: 0.7923 (tp) REVERT: N 365 MET cc_start: 0.8380 (ttt) cc_final: 0.7434 (pmt) REVERT: O 18 ILE cc_start: 0.8768 (pt) cc_final: 0.8533 (pp) REVERT: O 24 TYR cc_start: 0.8839 (m-80) cc_final: 0.8545 (m-80) REVERT: O 144 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8948 (p) REVERT: O 175 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7983 (ttp-110) REVERT: O 409 TRP cc_start: 0.8669 (m100) cc_final: 0.8375 (m100) outliers start: 37 outliers final: 22 residues processed: 135 average time/residue: 1.1520 time to fit residues: 166.8247 Evaluate side-chains 131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 242 LEU 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 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 368 ILE 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 84 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.0270 chunk 34 optimal weight: 10.0000 chunk 71 optimal weight: 0.0060 chunk 17 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 overall best weight: 3.4060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.102172 restraints weight = 10951.437| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.70 r_work: 0.2938 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8827 Z= 0.180 Angle : 0.633 9.563 12024 Z= 0.325 Chirality : 0.047 0.241 1329 Planarity : 0.005 0.065 1549 Dihedral : 5.215 33.536 1202 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.57 % Allowed : 14.03 % Favored : 81.40 % 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: -0.75 (0.25), residues: 1102 helix: 1.23 (0.47), residues: 141 sheet: 0.13 (0.29), residues: 332 loop : -1.29 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 330 HIS 0.006 0.001 HIS N 41 PHE 0.017 0.001 PHE K 128 TYR 0.021 0.002 TYR O 308 ARG 0.004 0.001 ARG N 298 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 298) hydrogen bonds : angle 4.88009 ( 807) SS BOND : bond 0.00413 ( 16) SS BOND : angle 1.90388 ( 32) covalent geometry : bond 0.00446 ( 8811) covalent geometry : angle 0.62640 (11992) *********************** 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 161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7664 (ptp) cc_final: 0.7123 (ptt) REVERT: K 121 LYS cc_start: 0.8445 (pptt) cc_final: 0.8239 (tmmt) REVERT: K 190 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8210 (mttt) REVERT: K 196 PRO cc_start: 0.8427 (Cg_endo) cc_final: 0.8121 (Cg_exo) REVERT: K 267 TYR cc_start: 0.8341 (t80) cc_final: 0.7970 (t80) REVERT: K 270 GLU cc_start: 0.6587 (pm20) cc_final: 0.6372 (pm20) REVERT: N 66 MET cc_start: 0.9522 (ttp) cc_final: 0.9295 (ttt) REVERT: N 88 ARG cc_start: 0.8856 (mtm110) cc_final: 0.7017 (mtt180) REVERT: N 173 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7640 (mt-10) REVERT: N 197 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7220 (tt) REVERT: N 207 ILE cc_start: 0.8227 (mt) cc_final: 0.7892 (tp) REVERT: N 239 ASN cc_start: 0.8214 (t0) cc_final: 0.7576 (t0) REVERT: N 365 MET cc_start: 0.8439 (ttt) cc_final: 0.7495 (pmt) REVERT: O 18 ILE cc_start: 0.8768 (pt) cc_final: 0.8529 (pp) REVERT: O 24 TYR cc_start: 0.8903 (m-80) cc_final: 0.8655 (m-80) REVERT: O 175 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7973 (ttp-110) REVERT: O 263 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7719 (m) outliers start: 43 outliers final: 28 residues processed: 142 average time/residue: 1.5941 time to fit residues: 242.2377 Evaluate side-chains 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 190 LYS 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 M residue 52 LEU 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 250 THR Chi-restraints excluded: chain N residue 277 THR 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 80 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 144 THR Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 208 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 35 optimal weight: 0.0170 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 0.0270 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.5280 ------------------------------------------------------------------------------- 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 ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 ASN O 439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104061 restraints weight = 10882.238| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.69 r_work: 0.2959 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8827 Z= 0.112 Angle : 0.573 8.120 12024 Z= 0.295 Chirality : 0.044 0.208 1329 Planarity : 0.005 0.066 1549 Dihedral : 4.957 33.808 1202 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.83 % Allowed : 14.98 % Favored : 81.19 % 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: -0.59 (0.25), residues: 1102 helix: 1.44 (0.47), residues: 143 sheet: 0.17 (0.30), residues: 327 loop : -1.16 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 89 HIS 0.003 0.001 HIS N 256 PHE 0.017 0.001 PHE K 128 TYR 0.023 0.001 TYR O 434 ARG 0.003 0.000 ARG M 41 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 298) hydrogen bonds : angle 4.70400 ( 807) SS BOND : bond 0.00432 ( 16) SS BOND : angle 1.54237 ( 32) covalent geometry : bond 0.00265 ( 8811) covalent geometry : angle 0.56816 (11992) *********************** 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 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7633 (ptp) cc_final: 0.7267 (ptt) REVERT: K 121 LYS cc_start: 0.8450 (pptt) cc_final: 0.8243 (tmmt) REVERT: K 190 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8198 (mtpt) REVERT: K 196 PRO cc_start: 0.8254 (Cg_endo) cc_final: 0.8017 (Cg_exo) REVERT: K 242 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8466 (mt) REVERT: K 267 TYR cc_start: 0.8315 (t80) cc_final: 0.7939 (t80) REVERT: K 270 GLU cc_start: 0.6625 (pm20) cc_final: 0.6358 (pm20) REVERT: N 42 ASP cc_start: 0.8260 (m-30) cc_final: 0.8036 (m-30) REVERT: N 66 MET cc_start: 0.9455 (ttp) cc_final: 0.9116 (ttt) REVERT: N 88 ARG cc_start: 0.8799 (mtm110) cc_final: 0.6980 (mtt180) REVERT: N 197 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7224 (tt) REVERT: N 365 MET cc_start: 0.8350 (ttt) cc_final: 0.7407 (pmt) REVERT: O 18 ILE cc_start: 0.8712 (pt) cc_final: 0.8481 (pp) REVERT: O 24 TYR cc_start: 0.8822 (m-80) cc_final: 0.8559 (m-80) outliers start: 36 outliers final: 22 residues processed: 129 average time/residue: 1.0892 time to fit residues: 151.3896 Evaluate side-chains 128 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 169 LYS Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 190 LYS 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 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 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 80 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 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 327 LYS 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: 7.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103697 restraints weight = 11078.856| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.62 r_work: 0.2967 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8827 Z= 0.123 Angle : 0.575 9.355 12024 Z= 0.295 Chirality : 0.044 0.171 1329 Planarity : 0.005 0.067 1549 Dihedral : 4.916 34.413 1202 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.51 % Allowed : 15.62 % Favored : 80.87 % 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: -0.52 (0.25), residues: 1102 helix: 1.41 (0.47), residues: 144 sheet: 0.24 (0.30), residues: 327 loop : -1.11 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 89 HIS 0.003 0.001 HIS N 256 PHE 0.022 0.001 PHE K 128 TYR 0.020 0.001 TYR O 308 ARG 0.002 0.000 ARG N 298 Details of bonding type rmsd hydrogen bonds : bond 0.02737 ( 298) hydrogen bonds : angle 4.62078 ( 807) SS BOND : bond 0.00365 ( 16) SS BOND : angle 1.27158 ( 32) covalent geometry : bond 0.00296 ( 8811) covalent geometry : angle 0.57209 (11992) *********************** 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 137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7679 (ptp) cc_final: 0.7188 (ptt) REVERT: K 121 LYS cc_start: 0.8471 (pptt) cc_final: 0.8265 (tmmt) REVERT: K 123 GLU cc_start: 0.7069 (pp20) cc_final: 0.6465 (pp20) REVERT: K 190 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8225 (mtpt) REVERT: K 196 PRO cc_start: 0.8116 (Cg_endo) cc_final: 0.7884 (Cg_exo) REVERT: K 257 MET cc_start: 0.9050 (ptp) cc_final: 0.8789 (mpp) REVERT: K 267 TYR cc_start: 0.8345 (t80) cc_final: 0.8010 (t80) REVERT: K 270 GLU cc_start: 0.6569 (pm20) cc_final: 0.6260 (pm20) REVERT: N 66 MET cc_start: 0.9439 (ttp) cc_final: 0.9213 (ttt) REVERT: N 88 ARG cc_start: 0.8805 (mtm110) cc_final: 0.6961 (mtt180) REVERT: N 197 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7228 (tt) REVERT: N 365 MET cc_start: 0.8369 (ttt) cc_final: 0.7436 (pmt) REVERT: O 18 ILE cc_start: 0.8716 (pt) cc_final: 0.8495 (pp) REVERT: O 24 TYR cc_start: 0.8790 (m-80) cc_final: 0.8468 (m-80) REVERT: O 175 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7968 (ttp-110) REVERT: O 345 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8070 (mm-30) outliers start: 33 outliers final: 25 residues processed: 125 average time/residue: 1.1552 time to fit residues: 154.6785 Evaluate side-chains 127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 190 LYS Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain N residue 11 LEU 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 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 84 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 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 290 VAL 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 433 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 0.0070 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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 ** N 160 ASN ** 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 = 0.3705 r_free = 0.3705 target = 0.148859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107246 restraints weight = 11151.517| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.63 r_work: 0.3004 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8827 Z= 0.090 Angle : 0.537 8.851 12024 Z= 0.276 Chirality : 0.043 0.173 1329 Planarity : 0.005 0.069 1549 Dihedral : 4.690 34.958 1202 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.34 % Allowed : 17.00 % Favored : 80.66 % 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: -0.38 (0.26), residues: 1102 helix: 1.57 (0.47), residues: 144 sheet: 0.37 (0.30), residues: 328 loop : -1.06 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 409 HIS 0.003 0.001 HIS N 256 PHE 0.021 0.001 PHE K 128 TYR 0.024 0.001 TYR O 434 ARG 0.003 0.000 ARG M 41 Details of bonding type rmsd hydrogen bonds : bond 0.02500 ( 298) hydrogen bonds : angle 4.46870 ( 807) SS BOND : bond 0.00291 ( 16) SS BOND : angle 1.12191 ( 32) covalent geometry : bond 0.00202 ( 8811) covalent geometry : angle 0.53494 (11992) *********************** 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 138 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 120 MET cc_start: 0.7689 (ptp) cc_final: 0.7319 (ptt) REVERT: K 196 PRO cc_start: 0.8091 (Cg_endo) cc_final: 0.7870 (Cg_exo) REVERT: K 242 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8497 (mt) REVERT: K 257 MET cc_start: 0.9044 (ptp) cc_final: 0.8694 (mpp) REVERT: K 267 TYR cc_start: 0.8273 (t80) cc_final: 0.7957 (t80) REVERT: N 21 ARG cc_start: 0.7737 (mmt90) cc_final: 0.5650 (mmm160) REVERT: N 66 MET cc_start: 0.9400 (ttp) cc_final: 0.9105 (ttt) REVERT: N 88 ARG cc_start: 0.8756 (mtm110) cc_final: 0.6956 (mtt180) REVERT: N 113 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8456 (mt-10) REVERT: N 197 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7176 (tt) REVERT: N 365 MET cc_start: 0.8261 (ttt) cc_final: 0.7428 (pmt) REVERT: O 18 ILE cc_start: 0.8662 (pt) cc_final: 0.8438 (pp) REVERT: O 24 TYR cc_start: 0.8700 (m-80) cc_final: 0.8407 (m-80) REVERT: O 175 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7979 (ttp-110) outliers start: 22 outliers final: 12 residues processed: 129 average time/residue: 1.5531 time to fit residues: 213.6293 Evaluate side-chains 119 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR 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 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 42 VAL 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 433 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 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 ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.144564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.101985 restraints weight = 11074.427| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.61 r_work: 0.2948 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8827 Z= 0.157 Angle : 0.605 11.301 12024 Z= 0.308 Chirality : 0.045 0.172 1329 Planarity : 0.005 0.067 1549 Dihedral : 4.903 35.771 1202 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.34 % Allowed : 18.07 % Favored : 79.60 % 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: -0.43 (0.25), residues: 1102 helix: 1.55 (0.47), residues: 144 sheet: 0.30 (0.29), residues: 340 loop : -1.10 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 409 HIS 0.005 0.001 HIS N 256 PHE 0.024 0.001 PHE K 128 TYR 0.019 0.001 TYR O 308 ARG 0.004 0.000 ARG N 298 Details of bonding type rmsd hydrogen bonds : bond 0.02802 ( 298) hydrogen bonds : angle 4.57386 ( 807) SS BOND : bond 0.00296 ( 16) SS BOND : angle 1.46764 ( 32) covalent geometry : bond 0.00388 ( 8811) covalent geometry : angle 0.60062 (11992) *********************** 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 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7865 (ptp) cc_final: 0.7394 (ptt) REVERT: K 267 TYR cc_start: 0.8338 (t80) cc_final: 0.8034 (t80) REVERT: N 88 ARG cc_start: 0.8798 (mtm110) cc_final: 0.6961 (mtt180) REVERT: N 197 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7220 (tt) REVERT: N 231 LEU cc_start: 0.8655 (mt) cc_final: 0.8415 (mt) REVERT: N 365 MET cc_start: 0.8285 (ttt) cc_final: 0.7422 (pmt) REVERT: O 18 ILE cc_start: 0.8745 (pt) cc_final: 0.8509 (pp) REVERT: O 24 TYR cc_start: 0.8819 (m-80) cc_final: 0.8509 (m-80) REVERT: O 175 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7910 (ttp-110) outliers start: 22 outliers final: 20 residues processed: 118 average time/residue: 1.1648 time to fit residues: 148.4229 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 : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR 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 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 377 LYS 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: 5.9990 chunk 86 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** N 160 ASN ** 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 = 0.3703 r_free = 0.3703 target = 0.148740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114895 restraints weight = 11042.893| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.78 r_work: 0.2944 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8827 Z= 0.094 Angle : 0.538 9.637 12024 Z= 0.275 Chirality : 0.043 0.169 1329 Planarity : 0.005 0.070 1549 Dihedral : 4.642 35.477 1202 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.59 % Allowed : 18.49 % 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: -0.35 (0.25), residues: 1102 helix: 1.82 (0.47), residues: 138 sheet: 0.40 (0.30), residues: 329 loop : -1.07 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 326 HIS 0.003 0.001 HIS N 256 PHE 0.018 0.001 PHE K 128 TYR 0.023 0.001 TYR O 434 ARG 0.002 0.000 ARG M 41 Details of bonding type rmsd hydrogen bonds : bond 0.02452 ( 298) hydrogen bonds : angle 4.45347 ( 807) SS BOND : bond 0.00236 ( 16) SS BOND : angle 1.01064 ( 32) covalent geometry : bond 0.00214 ( 8811) covalent geometry : angle 0.53613 (11992) ********************** 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 120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: K 120 MET cc_start: 0.7789 (ptp) cc_final: 0.7360 (ptt) REVERT: K 196 PRO cc_start: 0.7926 (Cg_endo) cc_final: 0.7688 (Cg_exo) REVERT: K 267 TYR cc_start: 0.8313 (t80) cc_final: 0.7978 (t80) REVERT: N 9 TYR cc_start: 0.8055 (m-80) cc_final: 0.7822 (m-10) REVERT: N 21 ARG cc_start: 0.7638 (mmt90) cc_final: 0.5530 (mmm160) REVERT: N 66 MET cc_start: 0.9431 (ttt) cc_final: 0.9193 (ttt) REVERT: N 88 ARG cc_start: 0.8879 (mtm110) cc_final: 0.7033 (mtt180) REVERT: N 113 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8561 (mt-10) REVERT: N 197 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7133 (tt) REVERT: N 365 MET cc_start: 0.8341 (ttt) cc_final: 0.7363 (pmt) REVERT: O 18 ILE cc_start: 0.8657 (pt) cc_final: 0.8418 (pp) REVERT: O 24 TYR cc_start: 0.8757 (m-80) cc_final: 0.8428 (m-80) REVERT: O 175 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.8078 (ttp-110) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 1.3185 time to fit residues: 157.0787 Evaluate side-chains 113 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 251 THR 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 63 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 50.0000 chunk 26 optimal weight: 6.9990 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 ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 GLN O 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099886 restraints weight = 11086.924| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.59 r_work: 0.2913 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8827 Z= 0.231 Angle : 0.676 11.748 12024 Z= 0.346 Chirality : 0.048 0.177 1329 Planarity : 0.005 0.068 1549 Dihedral : 5.212 36.872 1202 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.91 % Allowed : 18.28 % 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: -0.48 (0.25), residues: 1102 helix: 1.60 (0.48), residues: 138 sheet: 0.24 (0.29), residues: 341 loop : -1.11 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 202 HIS 0.006 0.001 HIS N 41 PHE 0.014 0.002 PHE N 328 TYR 0.020 0.002 TYR O 308 ARG 0.005 0.001 ARG N 298 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 298) hydrogen bonds : angle 4.79959 ( 807) SS BOND : bond 0.00329 ( 16) SS BOND : angle 1.80089 ( 32) covalent geometry : bond 0.00576 ( 8811) covalent geometry : angle 0.67016 (11992) =============================================================================== Job complete usr+sys time: 9592.07 seconds wall clock time: 171 minutes 18.84 seconds (10278.84 seconds total)