Starting phenix.real_space_refine on Tue Mar 3 22:18:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pb1_20285/03_2026/6pb1_20285.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pb1_20285/03_2026/6pb1_20285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pb1_20285/03_2026/6pb1_20285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pb1_20285/03_2026/6pb1_20285.map" model { file = "/net/cci-nas-00/data/ceres_data/6pb1_20285/03_2026/6pb1_20285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pb1_20285/03_2026/6pb1_20285.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5642 2.51 5 N 1507 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8785 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2363 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain: "U" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 330 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "A" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1892 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 202 Unusual residues: {'CLR': 4, 'PLM': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 1.79, per 1000 atoms: 0.20 Number of scatterers: 8785 At special positions: 0 Unit cell: (106.47, 96.33, 137.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1584 8.00 N 1507 7.00 C 5642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS P 184 " - pdb=" SG CYS P 254 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 330.2 milliseconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 42.7% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'P' and resid 110 through 141 removed outlier: 3.988A pdb=" N ARG P 114 " --> pdb=" O ASP P 110 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA P 133 " --> pdb=" O ALA P 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 171 removed outlier: 4.227A pdb=" N LEU P 171 " --> pdb=" O PHE P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 179 Processing helix chain 'P' and resid 181 through 214 removed outlier: 3.843A pdb=" N ARG P 185 " --> pdb=" O GLU P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 222 removed outlier: 3.576A pdb=" N ARG P 221 " --> pdb=" O SER P 218 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU P 222 " --> pdb=" O THR P 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 218 through 222' Processing helix chain 'P' and resid 223 through 232 removed outlier: 3.507A pdb=" N PHE P 227 " --> pdb=" O ARG P 223 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 248 removed outlier: 3.673A pdb=" N TYR P 248 " --> pdb=" O ILE P 244 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 256 Processing helix chain 'P' and resid 265 through 298 removed outlier: 3.785A pdb=" N GLN P 269 " --> pdb=" O ASP P 265 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY P 270 " --> pdb=" O TYR P 266 " (cutoff:3.500A) Proline residue: P 271 - end of helix removed outlier: 4.080A pdb=" N ALA P 296 " --> pdb=" O THR P 292 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 316 Processing helix chain 'P' and resid 320 through 325 removed outlier: 3.655A pdb=" N TYR P 323 " --> pdb=" O GLY P 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 350 removed outlier: 3.854A pdb=" N GLN P 337 " --> pdb=" O ASP P 333 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE P 338 " --> pdb=" O ASP P 334 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET P 339 " --> pdb=" O LEU P 335 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE P 350 " --> pdb=" O PHE P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 361 Processing helix chain 'P' and resid 363 through 382 Processing helix chain 'U' and resid 8 through 40 removed outlier: 3.587A pdb=" N THR U 16 " --> pdb=" O HIS U 12 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU U 17 " --> pdb=" O LEU U 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.882A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.743A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.518A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.502A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.298A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.845A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.515A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.879A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.102A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.520A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.228A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.061A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.870A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 5.710A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.779A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.506A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.727A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.500A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2774 1.34 - 1.46: 1744 1.46 - 1.58: 4386 1.58 - 1.70: 0 1.70 - 1.81: 72 Bond restraints: 8976 Sorted by residual: bond pdb=" CA LEU P 171 " pdb=" C LEU P 171 " ideal model delta sigma weight residual 1.523 1.548 -0.024 1.30e-02 5.92e+03 3.51e+00 bond pdb=" C ILE P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 bond pdb=" CA VAL P 172 " pdb=" C VAL P 172 " ideal model delta sigma weight residual 1.522 1.543 -0.021 1.35e-02 5.49e+03 2.47e+00 bond pdb=" C5 CLR P 401 " pdb=" C6 CLR P 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C5 CLR P 403 " pdb=" C6 CLR P 403 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 8971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 11887 2.41 - 4.82: 228 4.82 - 7.22: 28 7.22 - 9.63: 3 9.63 - 12.04: 1 Bond angle restraints: 12147 Sorted by residual: angle pdb=" N VAL P 172 " pdb=" CA VAL P 172 " pdb=" C VAL P 172 " ideal model delta sigma weight residual 109.63 121.67 -12.04 1.44e+00 4.82e-01 6.99e+01 angle pdb=" N LEU P 171 " pdb=" CA LEU P 171 " pdb=" C LEU P 171 " ideal model delta sigma weight residual 111.28 119.28 -8.00 1.09e+00 8.42e-01 5.39e+01 angle pdb=" CA ILE P 234 " pdb=" C ILE P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 118.88 123.00 -4.12 1.54e+00 4.22e-01 7.16e+00 angle pdb=" CA PHE P 236 " pdb=" C PHE P 236 " pdb=" N PRO P 237 " ideal model delta sigma weight residual 118.44 122.67 -4.23 1.59e+00 3.96e-01 7.09e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.21 -3.81 1.45e+00 4.76e-01 6.92e+00 ... (remaining 12142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 5293 15.06 - 30.12: 173 30.12 - 45.18: 47 45.18 - 60.23: 15 60.23 - 75.29: 7 Dihedral angle restraints: 5535 sinusoidal: 2418 harmonic: 3117 Sorted by residual: dihedral pdb=" CA PRO P 235 " pdb=" C PRO P 235 " pdb=" N PHE P 236 " pdb=" CA PHE P 236 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN N 35 " pdb=" C ASN N 35 " pdb=" N TRP N 36 " pdb=" CA TRP N 36 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 5532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1216 0.084 - 0.168: 113 0.168 - 0.252: 15 0.252 - 0.336: 3 0.336 - 0.420: 5 Chirality restraints: 1352 Sorted by residual: chirality pdb=" C14 CLR P 403 " pdb=" C13 CLR P 403 " pdb=" C15 CLR P 403 " pdb=" C8 CLR P 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" C14 CLR P 401 " pdb=" C13 CLR P 401 " pdb=" C15 CLR P 401 " pdb=" C8 CLR P 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C14 CLR P 402 " pdb=" C13 CLR P 402 " pdb=" C15 CLR P 402 " pdb=" C8 CLR P 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 1349 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN P 170 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C GLN P 170 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN P 170 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU P 171 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 314 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C VAL P 314 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL P 314 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU P 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 301 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C VAL A 301 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 301 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 302 " 0.015 2.00e-02 2.50e+03 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2334 2.81 - 3.33: 7328 3.33 - 3.86: 13870 3.86 - 4.38: 16228 4.38 - 4.90: 28550 Nonbonded interactions: 68310 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.335 3.040 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.346 3.120 nonbonded pdb=" OG SER P 297 " pdb=" NH1 ARG A 385 " model vdw 2.371 3.120 ... (remaining 68305 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8979 Z= 0.185 Angle : 0.789 12.041 12153 Z= 0.422 Chirality : 0.059 0.420 1352 Planarity : 0.006 0.063 1523 Dihedral : 9.366 75.292 3506 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.20), residues: 1051 helix: -1.45 (0.19), residues: 420 sheet: -1.51 (0.30), residues: 226 loop : -2.58 (0.23), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 118 TYR 0.026 0.002 TYR N 115 PHE 0.026 0.002 PHE P 327 TRP 0.031 0.003 TRP B 169 HIS 0.016 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8976) covalent geometry : angle 0.78778 (12147) SS BOND : bond 0.00383 ( 3) SS BOND : angle 2.11910 ( 6) hydrogen bonds : bond 0.12449 ( 429) hydrogen bonds : angle 5.94643 ( 1239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.321 Fit side-chains REVERT: P 234 ILE cc_start: 0.7291 (mt) cc_final: 0.6944 (mt) REVERT: A 300 LYS cc_start: 0.6362 (mmtt) cc_final: 0.6090 (pptt) REVERT: A 391 TYR cc_start: 0.7778 (m-80) cc_final: 0.7541 (m-80) REVERT: B 188 MET cc_start: 0.7941 (mmm) cc_final: 0.7710 (mmt) REVERT: N 80 TYR cc_start: 0.6023 (m-80) cc_final: 0.5772 (m-80) REVERT: N 110 VAL cc_start: 0.7114 (t) cc_final: 0.6901 (m) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.5678 time to fit residues: 144.8822 Evaluate side-chains 146 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.0970 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 152 HIS P 304 GLN P 351 GLN P 381 HIS A 59 GLN A 267 GLN A 278 ASN A 387 HIS B 266 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.188580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.155303 restraints weight = 10719.808| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.60 r_work: 0.3758 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8979 Z= 0.101 Angle : 0.501 7.016 12153 Z= 0.256 Chirality : 0.040 0.138 1352 Planarity : 0.004 0.043 1523 Dihedral : 6.938 59.365 1504 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.22 % Allowed : 11.82 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1051 helix: 0.78 (0.24), residues: 430 sheet: -1.16 (0.31), residues: 228 loop : -1.97 (0.26), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 385 TYR 0.014 0.001 TYR A 37 PHE 0.015 0.001 PHE P 358 TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8976) covalent geometry : angle 0.50090 (12147) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.39966 ( 6) hydrogen bonds : bond 0.03457 ( 429) hydrogen bonds : angle 4.14387 ( 1239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.256 Fit side-chains REVERT: P 109 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.5562 (p90) REVERT: P 234 ILE cc_start: 0.7454 (mt) cc_final: 0.7022 (mt) REVERT: P 236 PHE cc_start: 0.6844 (t80) cc_final: 0.6443 (t80) REVERT: P 252 GLU cc_start: 0.8162 (pp20) cc_final: 0.7835 (pp20) REVERT: U 24 GLN cc_start: 0.7231 (tp40) cc_final: 0.6574 (tp-100) REVERT: U 28 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: A 221 MET cc_start: 0.8075 (ttm) cc_final: 0.7599 (tpp) REVERT: A 310 ASP cc_start: 0.7808 (t70) cc_final: 0.7013 (p0) REVERT: A 341 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7911 (mp) REVERT: B 17 GLN cc_start: 0.7679 (tp-100) cc_final: 0.7403 (tp-100) REVERT: B 96 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7405 (ptp-170) REVERT: B 188 MET cc_start: 0.8743 (mmm) cc_final: 0.8495 (mmt) REVERT: B 234 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: B 259 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: N 68 PHE cc_start: 0.7988 (m-80) cc_final: 0.7730 (m-80) outliers start: 30 outliers final: 10 residues processed: 182 average time/residue: 0.5411 time to fit residues: 105.1890 Evaluate side-chains 157 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 0.0000 chunk 67 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.185300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.151549 restraints weight = 10597.540| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.58 r_work: 0.3675 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8979 Z= 0.093 Angle : 0.457 7.360 12153 Z= 0.238 Chirality : 0.039 0.132 1352 Planarity : 0.003 0.040 1523 Dihedral : 6.661 57.993 1504 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.87 % Allowed : 13.75 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1051 helix: 1.77 (0.25), residues: 432 sheet: -0.97 (0.31), residues: 227 loop : -1.63 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 373 TYR 0.013 0.001 TYR A 37 PHE 0.013 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8976) covalent geometry : angle 0.45690 (12147) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.59873 ( 6) hydrogen bonds : bond 0.03240 ( 429) hydrogen bonds : angle 3.83124 ( 1239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.293 Fit side-chains REVERT: P 109 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5532 (p90) REVERT: P 234 ILE cc_start: 0.7673 (mt) cc_final: 0.7081 (mt) REVERT: P 236 PHE cc_start: 0.6760 (t80) cc_final: 0.6263 (m-80) REVERT: P 252 GLU cc_start: 0.8256 (pp20) cc_final: 0.7739 (pp20) REVERT: P 338 ILE cc_start: 0.7101 (pt) cc_final: 0.6803 (mm) REVERT: U 24 GLN cc_start: 0.7311 (tp40) cc_final: 0.6613 (tp-100) REVERT: U 28 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: A 209 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7513 (pt0) REVERT: A 221 MET cc_start: 0.8099 (ttm) cc_final: 0.7617 (tpp) REVERT: A 370 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6947 (tm-30) REVERT: B 17 GLN cc_start: 0.7666 (tp-100) cc_final: 0.7408 (tp-100) REVERT: B 105 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8416 (t80) REVERT: B 175 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6736 (mp10) REVERT: B 188 MET cc_start: 0.8684 (mmm) cc_final: 0.8449 (mmt) REVERT: B 234 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7512 (m-80) REVERT: G 38 MET cc_start: 0.7405 (ttp) cc_final: 0.7077 (ttm) REVERT: N 69 THR cc_start: 0.8248 (m) cc_final: 0.7982 (t) outliers start: 36 outliers final: 15 residues processed: 177 average time/residue: 0.5261 time to fit residues: 100.0920 Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN P 198 ASN P 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.179183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145191 restraints weight = 10883.178| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.57 r_work: 0.3581 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8979 Z= 0.124 Angle : 0.493 8.643 12153 Z= 0.255 Chirality : 0.040 0.141 1352 Planarity : 0.003 0.040 1523 Dihedral : 6.746 55.993 1504 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.94 % Allowed : 14.93 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1051 helix: 2.12 (0.25), residues: 431 sheet: -0.64 (0.32), residues: 220 loop : -1.31 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.013 0.001 TYR A 37 PHE 0.012 0.001 PHE A 212 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8976) covalent geometry : angle 0.49314 (12147) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.62737 ( 6) hydrogen bonds : bond 0.03688 ( 429) hydrogen bonds : angle 3.85418 ( 1239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.323 Fit side-chains REVERT: P 109 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.6129 (p90) REVERT: P 234 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7558 (mt) REVERT: P 236 PHE cc_start: 0.6918 (t80) cc_final: 0.6441 (m-80) REVERT: P 252 GLU cc_start: 0.8451 (pp20) cc_final: 0.7978 (pp20) REVERT: P 338 ILE cc_start: 0.7126 (pt) cc_final: 0.6841 (mm) REVERT: P 348 GLN cc_start: 0.7834 (tt0) cc_final: 0.7619 (tt0) REVERT: U 24 GLN cc_start: 0.7271 (tp40) cc_final: 0.6550 (tp-100) REVERT: U 28 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: A 300 LYS cc_start: 0.5934 (mmtt) cc_final: 0.5703 (tttt) REVERT: A 370 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7066 (tm-30) REVERT: B 8 ARG cc_start: 0.7466 (mtm180) cc_final: 0.7260 (mmm-85) REVERT: B 17 GLN cc_start: 0.7675 (tp-100) cc_final: 0.7360 (tp-100) REVERT: B 105 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8487 (t80) REVERT: B 188 MET cc_start: 0.8687 (mmm) cc_final: 0.8442 (mmt) REVERT: B 197 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.7323 (mmm-85) REVERT: B 234 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: B 259 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: G 38 MET cc_start: 0.7375 (ttp) cc_final: 0.6992 (ttm) outliers start: 46 outliers final: 23 residues processed: 166 average time/residue: 0.5404 time to fit residues: 95.9330 Evaluate side-chains 157 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 324 MET Chi-restraints excluded: chain U residue 4 SER Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN P 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.178596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.144302 restraints weight = 10784.187| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.54 r_work: 0.3615 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8979 Z= 0.100 Angle : 0.464 7.524 12153 Z= 0.241 Chirality : 0.039 0.140 1352 Planarity : 0.003 0.040 1523 Dihedral : 6.433 52.552 1504 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.33 % Allowed : 18.15 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1051 helix: 2.31 (0.25), residues: 431 sheet: -0.53 (0.33), residues: 216 loop : -1.18 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 288 TYR 0.016 0.001 TYR N 60 PHE 0.012 0.001 PHE P 256 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8976) covalent geometry : angle 0.46407 (12147) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.59885 ( 6) hydrogen bonds : bond 0.03292 ( 429) hydrogen bonds : angle 3.74254 ( 1239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.326 Fit side-chains REVERT: P 109 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.6181 (p90) REVERT: P 234 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7597 (mt) REVERT: P 236 PHE cc_start: 0.6925 (t80) cc_final: 0.6454 (m-80) REVERT: P 252 GLU cc_start: 0.8462 (pp20) cc_final: 0.8000 (pp20) REVERT: U 24 GLN cc_start: 0.7289 (tp40) cc_final: 0.6653 (tp40) REVERT: U 28 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: A 300 LYS cc_start: 0.5966 (mmtt) cc_final: 0.5737 (tttt) REVERT: A 370 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7053 (tm-30) REVERT: B 17 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7417 (tp-100) REVERT: B 105 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8440 (t80) REVERT: B 175 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6832 (mp10) REVERT: B 188 MET cc_start: 0.8686 (mmm) cc_final: 0.8473 (mmt) REVERT: B 259 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: G 38 MET cc_start: 0.7368 (ttp) cc_final: 0.7021 (ttm) outliers start: 31 outliers final: 17 residues processed: 153 average time/residue: 0.5347 time to fit residues: 87.6251 Evaluate side-chains 149 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136104 restraints weight = 10983.368| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.55 r_work: 0.3483 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8979 Z= 0.154 Angle : 0.523 7.044 12153 Z= 0.271 Chirality : 0.041 0.145 1352 Planarity : 0.003 0.040 1523 Dihedral : 6.918 54.994 1504 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.08 % Allowed : 17.72 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.26), residues: 1051 helix: 2.19 (0.25), residues: 431 sheet: -0.30 (0.34), residues: 209 loop : -1.12 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 288 TYR 0.017 0.001 TYR N 60 PHE 0.013 0.002 PHE P 135 TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8976) covalent geometry : angle 0.52246 (12147) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.66427 ( 6) hydrogen bonds : bond 0.03924 ( 429) hydrogen bonds : angle 3.88291 ( 1239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.362 Fit side-chains REVERT: P 109 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.6174 (p90) REVERT: P 220 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6290 (pm20) REVERT: P 234 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7680 (mt) REVERT: P 252 GLU cc_start: 0.8511 (pp20) cc_final: 0.7848 (pp20) REVERT: U 24 GLN cc_start: 0.7131 (tp40) cc_final: 0.6458 (tp40) REVERT: U 28 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: A 300 LYS cc_start: 0.6195 (mmtt) cc_final: 0.5918 (tttt) REVERT: A 341 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7695 (mp) REVERT: A 370 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6985 (tp30) REVERT: B 17 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7332 (tp-100) REVERT: B 105 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8401 (t80) REVERT: B 175 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6642 (mp10) REVERT: B 188 MET cc_start: 0.8639 (mmm) cc_final: 0.8434 (mmt) REVERT: B 234 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: G 38 MET cc_start: 0.7259 (ttp) cc_final: 0.6904 (ttm) outliers start: 38 outliers final: 23 residues processed: 156 average time/residue: 0.5367 time to fit residues: 89.9121 Evaluate side-chains 157 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 145 ARG Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 4 SER Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.178569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145001 restraints weight = 10876.336| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.54 r_work: 0.3574 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8979 Z= 0.103 Angle : 0.474 8.893 12153 Z= 0.246 Chirality : 0.040 0.138 1352 Planarity : 0.003 0.040 1523 Dihedral : 6.578 55.630 1504 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.44 % Allowed : 18.90 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1051 helix: 2.40 (0.25), residues: 431 sheet: -0.28 (0.33), residues: 214 loop : -0.98 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 288 TYR 0.016 0.001 TYR N 60 PHE 0.013 0.001 PHE P 256 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8976) covalent geometry : angle 0.47359 (12147) SS BOND : bond 0.00192 ( 3) SS BOND : angle 0.61362 ( 6) hydrogen bonds : bond 0.03361 ( 429) hydrogen bonds : angle 3.77253 ( 1239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.345 Fit side-chains REVERT: P 220 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6281 (pm20) REVERT: P 234 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7642 (mt) REVERT: P 236 PHE cc_start: 0.6973 (t80) cc_final: 0.6386 (m-80) REVERT: P 252 GLU cc_start: 0.8482 (pp20) cc_final: 0.7787 (pp20) REVERT: U 24 GLN cc_start: 0.7178 (tp40) cc_final: 0.6523 (tp40) REVERT: U 28 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: A 300 LYS cc_start: 0.6193 (mmtt) cc_final: 0.5936 (tttt) REVERT: A 341 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7719 (mp) REVERT: A 370 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7029 (tp30) REVERT: B 17 GLN cc_start: 0.7710 (tp-100) cc_final: 0.7360 (tp-100) REVERT: B 105 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8379 (t80) REVERT: B 175 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: G 38 MET cc_start: 0.7225 (ttp) cc_final: 0.6874 (ttm) REVERT: N 115 TYR cc_start: 0.8458 (t80) cc_final: 0.8234 (t80) outliers start: 32 outliers final: 21 residues processed: 151 average time/residue: 0.4994 time to fit residues: 81.0686 Evaluate side-chains 152 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.171814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.137427 restraints weight = 10920.088| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.55 r_work: 0.3501 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8979 Z= 0.121 Angle : 0.487 7.180 12153 Z= 0.253 Chirality : 0.040 0.140 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.682 57.098 1504 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.97 % Allowed : 19.33 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1051 helix: 2.39 (0.25), residues: 431 sheet: -0.17 (0.34), residues: 208 loop : -0.95 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 371 TYR 0.016 0.001 TYR N 60 PHE 0.013 0.001 PHE P 256 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8976) covalent geometry : angle 0.48656 (12147) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.64771 ( 6) hydrogen bonds : bond 0.03570 ( 429) hydrogen bonds : angle 3.81583 ( 1239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.346 Fit side-chains REVERT: P 170 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7902 (tp40) REVERT: P 220 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6270 (pm20) REVERT: P 234 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7631 (mt) REVERT: P 236 PHE cc_start: 0.6932 (t80) cc_final: 0.6353 (m-80) REVERT: P 252 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7824 (pp20) REVERT: U 24 GLN cc_start: 0.7134 (tp40) cc_final: 0.6544 (tp40) REVERT: U 28 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: A 370 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6988 (tp30) REVERT: B 17 GLN cc_start: 0.7700 (tp-100) cc_final: 0.7334 (tp-100) REVERT: B 105 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8383 (t80) REVERT: B 175 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: G 38 MET cc_start: 0.7210 (ttp) cc_final: 0.6847 (ttm) REVERT: G 48 ASP cc_start: 0.8619 (t0) cc_final: 0.8210 (t0) REVERT: G 50 LEU cc_start: 0.7965 (mt) cc_final: 0.7654 (mt) REVERT: N 32 TYR cc_start: 0.8636 (m-80) cc_final: 0.8050 (m-80) outliers start: 37 outliers final: 23 residues processed: 149 average time/residue: 0.5178 time to fit residues: 82.9224 Evaluate side-chains 151 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 145 ARG Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 324 MET Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136796 restraints weight = 10885.866| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.54 r_work: 0.3549 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8979 Z= 0.125 Angle : 0.495 7.225 12153 Z= 0.257 Chirality : 0.041 0.139 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.766 59.787 1504 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.30 % Allowed : 19.23 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1051 helix: 2.41 (0.25), residues: 431 sheet: -0.17 (0.34), residues: 208 loop : -0.91 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 371 TYR 0.016 0.001 TYR N 60 PHE 0.020 0.001 PHE P 358 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8976) covalent geometry : angle 0.49515 (12147) SS BOND : bond 0.00268 ( 3) SS BOND : angle 0.62357 ( 6) hydrogen bonds : bond 0.03630 ( 429) hydrogen bonds : angle 3.83434 ( 1239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.326 Fit side-chains REVERT: P 220 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6302 (pm20) REVERT: P 234 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7721 (mt) REVERT: P 244 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7548 (mp) REVERT: P 252 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7733 (pp20) REVERT: U 24 GLN cc_start: 0.7165 (tp40) cc_final: 0.6497 (tp-100) REVERT: U 28 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: A 370 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7014 (tp30) REVERT: B 17 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7347 (tp-100) REVERT: B 105 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8398 (t80) REVERT: B 175 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: G 38 MET cc_start: 0.7244 (ttp) cc_final: 0.6877 (ttm) REVERT: G 48 ASP cc_start: 0.8606 (t0) cc_final: 0.8209 (t0) REVERT: G 50 LEU cc_start: 0.8026 (mt) cc_final: 0.7722 (mt) REVERT: N 32 TYR cc_start: 0.8625 (m-80) cc_final: 0.7991 (m-80) outliers start: 40 outliers final: 24 residues processed: 147 average time/residue: 0.5573 time to fit residues: 87.5349 Evaluate side-chains 153 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 145 ARG Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 62 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.173442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140014 restraints weight = 10878.224| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.51 r_work: 0.3567 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8979 Z= 0.110 Angle : 0.484 7.338 12153 Z= 0.252 Chirality : 0.040 0.137 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.612 58.740 1504 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.33 % Allowed : 20.41 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1051 helix: 2.53 (0.25), residues: 430 sheet: -0.13 (0.34), residues: 208 loop : -0.90 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 371 TYR 0.015 0.001 TYR N 60 PHE 0.019 0.001 PHE P 358 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8976) covalent geometry : angle 0.48364 (12147) SS BOND : bond 0.00236 ( 3) SS BOND : angle 0.79408 ( 6) hydrogen bonds : bond 0.03466 ( 429) hydrogen bonds : angle 3.79540 ( 1239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.357 Fit side-chains REVERT: P 220 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6300 (pm20) REVERT: P 234 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7690 (mt) REVERT: P 236 PHE cc_start: 0.7043 (t80) cc_final: 0.6458 (m-80) REVERT: P 252 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7748 (pp20) REVERT: U 24 GLN cc_start: 0.7225 (tp40) cc_final: 0.6642 (tp40) REVERT: U 28 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: A 370 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6964 (tp30) REVERT: B 14 LEU cc_start: 0.6982 (mt) cc_final: 0.6728 (mp) REVERT: B 17 GLN cc_start: 0.7722 (tp-100) cc_final: 0.7361 (tp-100) REVERT: B 105 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8394 (t80) REVERT: B 175 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: G 38 MET cc_start: 0.7247 (ttp) cc_final: 0.6879 (ttm) REVERT: G 48 ASP cc_start: 0.8594 (t0) cc_final: 0.8199 (t0) REVERT: G 50 LEU cc_start: 0.7971 (mt) cc_final: 0.7676 (mt) REVERT: N 32 TYR cc_start: 0.8581 (m-80) cc_final: 0.7994 (m-80) outliers start: 31 outliers final: 22 residues processed: 144 average time/residue: 0.5483 time to fit residues: 84.3615 Evaluate side-chains 147 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 145 ARG Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 252 GLU Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.170278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136255 restraints weight = 10786.199| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.51 r_work: 0.3536 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8979 Z= 0.143 Angle : 0.524 11.427 12153 Z= 0.270 Chirality : 0.041 0.141 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.723 54.468 1504 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.54 % Allowed : 20.19 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.26), residues: 1051 helix: 2.45 (0.25), residues: 430 sheet: -0.25 (0.34), residues: 215 loop : -0.85 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 371 TYR 0.022 0.001 TYR N 60 PHE 0.022 0.002 PHE P 358 TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS P 174 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8976) covalent geometry : angle 0.52369 (12147) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.73450 ( 6) hydrogen bonds : bond 0.03807 ( 429) hydrogen bonds : angle 3.88529 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3098.43 seconds wall clock time: 53 minutes 26.52 seconds (3206.52 seconds total)