Starting phenix.real_space_refine on Fri Sep 11 10:20:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pb1_20285/09_2026/6pb1_20285.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pb1_20285/09_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_20285/09_2026/6pb1_20285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pb1_20285/09_2026/6pb1_20285.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pb1_20285/09_2026/6pb1_20285.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pb1_20285/09_2026/6pb1_20285.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pb1_20285/09_2026/6pb1_20285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pb1_20285/09_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-2.2.1-6174/lib/python3.11/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: 1.93, per 1000 atoms: 0.22 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: 0.81 Conformation dependent library (CDL) restraints added in 322.9 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: 0.25 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: 1.47 Time building geometry restraints manager: 1.02 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: 5092 15.06 - 30.12: 165 30.12 - 45.18: 41 45.18 - 60.23: 6 60.23 - 75.29: 7 Dihedral angle restraints: 5311 sinusoidal: 2194 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 5308 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: 0.680 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.330 Find NCS groups from input model: 0.040 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:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 8.983 75.292 3282 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/Z covalent geometry : bond 0.00345 / 0.18 ( 8976) covalent geometry : angle 0.78778 / 0.42 (12147) SS BOND : bond 0.00383 / 0.19 ( 3) SS BOND : angle 2.11910 / 1.36 ( 6) hydrogen bonds : bond 0.12449 / 9.06 ( 429) hydrogen bonds : angle 5.94643 / 4.49 ( 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 : 0.332 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: 0.5569 time to fit residues: 142.4078 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 : 0.356 ------------------------------------------------------------------------------- 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... 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 = 0.4283 r_free = 0.4283 target = 0.188590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.155078 restraints weight = 10720.045| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.61 r_work: 0.3758 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8979 Z= 0.102 Angle : 0.500 6.979 12153 Z= 0.257 Chirality : 0.040 0.136 1352 Planarity : 0.004 0.043 1523 Dihedral : 4.915 57.043 1280 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.22 % Allowed : 11.92 % Favored : 84.85 % 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: -0.94 (0.24), residues: 1051 helix: 0.84 (0.24), residues: 431 sheet: -1.16 (0.31), residues: 227 loop : -1.90 (0.26), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.014 0.001 TYR A 37 PHE 0.016 0.001 PHE P 358 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 8976) covalent geometry : angle 0.50047 / 0.26 (12147) SS BOND : bond 0.00238 / 0.12 ( 3) SS BOND : angle 0.40535 / 0.24 ( 6) hydrogen bonds : bond 0.03462 / 2.28 ( 429) hydrogen bonds : angle 4.09921 / 3.04 ( 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 199 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: P 109 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5560 (p90) REVERT: P 234 ILE cc_start: 0.7461 (mt) cc_final: 0.7015 (mt) REVERT: P 236 PHE cc_start: 0.6843 (t80) cc_final: 0.6485 (t80) REVERT: P 252 GLU cc_start: 0.8137 (pp20) cc_final: 0.7819 (pp20) REVERT: U 24 GLN cc_start: 0.7222 (tp40) cc_final: 0.6574 (tp-100) REVERT: U 28 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: A 221 MET cc_start: 0.8077 (ttm) cc_final: 0.7609 (tpp) REVERT: A 310 ASP cc_start: 0.7796 (t70) cc_final: 0.6984 (p0) REVERT: A 341 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7872 (mp) REVERT: B 17 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7399 (tp-100) REVERT: B 96 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7407 (ptp-170) REVERT: B 188 MET cc_start: 0.8712 (mmm) cc_final: 0.8474 (mmt) REVERT: B 234 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: N 68 PHE cc_start: 0.7991 (m-80) cc_final: 0.7727 (m-80) outliers start: 30 outliers final: 12 residues processed: 185 average time/residue: 0.5490 time to fit residues: 108.5082 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 A residue 347 ARG 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 334 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 170 GLN P 198 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140180 restraints weight = 10809.740| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.56 r_work: 0.3568 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8979 Z= 0.132 Angle : 0.496 7.116 12153 Z= 0.260 Chirality : 0.041 0.157 1352 Planarity : 0.003 0.040 1523 Dihedral : 4.885 48.634 1280 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.62 % Allowed : 13.43 % Favored : 81.95 % 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: -0.09 (0.25), residues: 1051 helix: 1.69 (0.25), residues: 434 sheet: -0.75 (0.32), residues: 216 loop : -1.64 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 373 TYR 0.012 0.001 TYR A 37 PHE 0.014 0.002 PHE A 212 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 8976) covalent geometry : angle 0.49630 / 0.26 (12147) SS BOND : bond 0.00278 / 0.14 ( 3) SS BOND : angle 0.64583 / 0.40 ( 6) hydrogen bonds : bond 0.03791 / 2.52 ( 429) hydrogen bonds : angle 3.98599 / 2.94 ( 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 191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.232 Fit side-chains REVERT: P 109 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.6060 (p90) REVERT: P 234 ILE cc_start: 0.7831 (mt) cc_final: 0.7214 (mt) REVERT: P 236 PHE cc_start: 0.6867 (t80) cc_final: 0.6389 (m-80) REVERT: P 252 GLU cc_start: 0.8358 (pp20) cc_final: 0.8106 (pp20) REVERT: U 24 GLN cc_start: 0.7241 (tp40) cc_final: 0.6664 (tp40) REVERT: U 28 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: A 35 GLN cc_start: 0.6156 (mm-40) cc_final: 0.5939 (mm-40) REVERT: A 209 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7655 (pt0) REVERT: A 370 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6953 (tm-30) REVERT: B 17 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7341 (tp-100) REVERT: B 55 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8698 (mt) REVERT: B 96 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7316 (ptp-170) REVERT: B 105 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8441 (t80) REVERT: B 188 MET cc_start: 0.8657 (mmm) cc_final: 0.8407 (mmt) REVERT: B 214 ARG cc_start: 0.7429 (mmt180) cc_final: 0.7188 (mmt180) REVERT: B 234 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: G 38 MET cc_start: 0.7357 (ttp) cc_final: 0.6983 (ttm) REVERT: N 69 THR cc_start: 0.8285 (m) cc_final: 0.7998 (t) outliers start: 43 outliers final: 19 residues processed: 170 average time/residue: 0.4778 time to fit residues: 87.4972 Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 215 MET 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 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG 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 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 329 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 170 GLN P 198 ASN P 351 GLN U 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.174824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141355 restraints weight = 10906.368| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.47 r_work: 0.3577 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8979 Z= 0.134 Angle : 0.500 6.256 12153 Z= 0.259 Chirality : 0.041 0.143 1352 Planarity : 0.003 0.040 1523 Dihedral : 4.845 34.302 1280 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.40 % Allowed : 16.00 % Favored : 79.59 % 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: 0.30 (0.25), residues: 1051 helix: 2.07 (0.25), residues: 427 sheet: -0.60 (0.33), residues: 208 loop : -1.38 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 371 TYR 0.013 0.001 TYR N 60 PHE 0.012 0.001 PHE P 256 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 8976) covalent geometry : angle 0.49975 / 0.26 (12147) SS BOND : bond 0.00326 / 0.16 ( 3) SS BOND : angle 0.64477 / 0.42 ( 6) hydrogen bonds : bond 0.03788 / 2.52 ( 429) hydrogen bonds : angle 3.94830 / 2.90 ( 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 185 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.327 Fit side-chains REVERT: P 109 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.6280 (p90) REVERT: P 202 MET cc_start: 0.8509 (mtm) cc_final: 0.8307 (mtm) REVERT: P 234 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7797 (mt) REVERT: P 236 PHE cc_start: 0.7099 (t80) cc_final: 0.6525 (m-80) REVERT: P 252 GLU cc_start: 0.8520 (pp20) cc_final: 0.8027 (pp20) REVERT: U 24 GLN cc_start: 0.7317 (tp40) cc_final: 0.6718 (tp40) REVERT: U 28 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: A 35 GLN cc_start: 0.6530 (mm-40) cc_final: 0.6296 (mm-40) REVERT: A 300 LYS cc_start: 0.6121 (mmtt) cc_final: 0.5815 (tttt) REVERT: A 370 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7126 (tm-30) REVERT: A 372 ILE cc_start: 0.8337 (mp) cc_final: 0.7878 (pt) REVERT: B 17 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7409 (tp-100) REVERT: B 55 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8817 (mt) REVERT: B 59 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: B 96 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6909 (ptp-170) REVERT: B 105 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8543 (t80) REVERT: B 175 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6787 (mp10) REVERT: B 188 MET cc_start: 0.8767 (mmm) cc_final: 0.8531 (mmt) REVERT: B 234 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: B 259 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: G 38 MET cc_start: 0.7446 (ttp) cc_final: 0.7085 (ttm) outliers start: 41 outliers final: 22 residues processed: 164 average time/residue: 0.5206 time to fit residues: 91.7979 Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 244 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 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.179817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.146047 restraints weight = 10695.065| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.55 r_work: 0.3598 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8979 Z= 0.097 Angle : 0.464 7.353 12153 Z= 0.240 Chirality : 0.039 0.138 1352 Planarity : 0.003 0.040 1523 Dihedral : 4.463 32.983 1280 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.54 % Allowed : 17.62 % Favored : 78.84 % 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: 2.40 (0.25), residues: 424 sheet: -0.50 (0.33), residues: 213 loop : -1.24 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 288 TYR 0.016 0.001 TYR N 60 PHE 0.014 0.001 PHE P 256 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 8976) covalent geometry : angle 0.46376 / 0.24 (12147) SS BOND : bond 0.00211 / 0.10 ( 3) SS BOND : angle 0.60997 / 0.43 ( 6) hydrogen bonds : bond 0.03264 / 2.18 ( 429) hydrogen bonds : angle 3.78325 / 2.77 ( 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 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.281 Fit side-chains REVERT: P 109 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.6184 (p90) REVERT: P 234 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7721 (mt) REVERT: P 236 PHE cc_start: 0.6990 (t80) cc_final: 0.6442 (m-80) REVERT: P 252 GLU cc_start: 0.8453 (pp20) cc_final: 0.7961 (pp20) REVERT: U 24 GLN cc_start: 0.7245 (tp40) cc_final: 0.6608 (tp40) REVERT: U 28 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: A 35 GLN cc_start: 0.6261 (mm-40) cc_final: 0.5919 (mm-40) REVERT: A 300 LYS cc_start: 0.6115 (mmtt) cc_final: 0.5865 (tttt) REVERT: A 370 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6949 (tp30) REVERT: B 17 GLN cc_start: 0.7722 (tp-100) cc_final: 0.7389 (tp-100) REVERT: B 55 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8738 (mt) REVERT: B 105 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8454 (t80) REVERT: B 134 ARG cc_start: 0.6617 (mmm160) cc_final: 0.6299 (mmm160) REVERT: B 175 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6832 (mp10) REVERT: B 188 MET cc_start: 0.8675 (mmm) cc_final: 0.8469 (mmt) REVERT: B 259 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6852 (pm20) REVERT: G 38 MET cc_start: 0.7285 (ttp) cc_final: 0.6947 (ttm) outliers start: 33 outliers final: 16 residues processed: 156 average time/residue: 0.5009 time to fit residues: 84.1078 Evaluate side-chains 151 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 55 LEU 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 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 54 SER Chi-restraints excluded: chain N residue 70 ILE 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: 4.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 170 GLN ** P 198 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 = 0.4117 r_free = 0.4117 target = 0.173448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139339 restraints weight = 10976.860| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.54 r_work: 0.3584 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8979 Z= 0.121 Angle : 0.490 7.507 12153 Z= 0.252 Chirality : 0.040 0.140 1352 Planarity : 0.003 0.039 1523 Dihedral : 4.636 30.100 1280 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.30 % Allowed : 17.51 % 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: 0.75 (0.26), residues: 1051 helix: 2.43 (0.25), residues: 424 sheet: -0.32 (0.33), residues: 214 loop : -1.14 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 288 TYR 0.014 0.001 TYR N 60 PHE 0.014 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/Z covalent geometry : bond 0.00287 / 0.12 ( 8976) covalent geometry : angle 0.48963 / 0.25 (12147) SS BOND : bond 0.00257 / 0.13 ( 3) SS BOND : angle 0.59699 / 0.42 ( 6) hydrogen bonds : bond 0.03602 / 2.39 ( 429) hydrogen bonds : angle 3.81838 / 2.81 ( 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 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.368 Fit side-chains REVERT: P 109 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.6382 (p90) REVERT: P 170 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.6502 (mp-120) REVERT: P 234 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7727 (mt) REVERT: P 236 PHE cc_start: 0.7016 (t80) cc_final: 0.6515 (m-80) REVERT: P 252 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7848 (pp20) REVERT: U 24 GLN cc_start: 0.7201 (tp40) cc_final: 0.6520 (tp40) REVERT: U 28 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: A 35 GLN cc_start: 0.6259 (mm-40) cc_final: 0.5910 (mm-40) REVERT: A 300 LYS cc_start: 0.6242 (mmtt) cc_final: 0.5958 (tttt) REVERT: A 370 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7068 (tp30) REVERT: B 17 GLN cc_start: 0.7755 (tp-100) cc_final: 0.7404 (tp-100) REVERT: B 55 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8747 (mt) REVERT: B 105 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8404 (t80) REVERT: B 134 ARG cc_start: 0.6625 (mmm160) cc_final: 0.6318 (mmm160) REVERT: B 175 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.6830 (mp10) REVERT: B 259 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: B 280 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7504 (tmtm) REVERT: G 38 MET cc_start: 0.7373 (ttp) cc_final: 0.7026 (ttm) REVERT: G 48 ASP cc_start: 0.8436 (t0) cc_final: 0.8035 (t0) REVERT: G 51 LEU cc_start: 0.7657 (mp) cc_final: 0.7275 (mp) outliers start: 40 outliers final: 21 residues processed: 156 average time/residue: 0.5234 time to fit residues: 87.7454 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 168 LEU 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 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 55 LEU 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 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 275 SER Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 334 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 170 GLN A 35 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.178724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145248 restraints weight = 10838.235| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.54 r_work: 0.3583 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3737 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= 0.097 Angle : 0.462 7.560 12153 Z= 0.239 Chirality : 0.039 0.136 1352 Planarity : 0.003 0.040 1523 Dihedral : 4.467 29.744 1280 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.30 % Allowed : 18.15 % Favored : 77.55 % 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: 2.57 (0.25), residues: 424 sheet: -0.22 (0.33), residues: 214 loop : -1.03 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 288 TYR 0.014 0.001 TYR N 60 PHE 0.015 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/Z covalent geometry : bond 0.00220 / 0.10 ( 8976) covalent geometry : angle 0.46213 / 0.24 (12147) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 0.61478 / 0.44 ( 6) hydrogen bonds : bond 0.03320 / 2.21 ( 429) hydrogen bonds : angle 3.74733 / 2.75 ( 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 166 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.370 Fit side-chains REVERT: P 234 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7656 (mt) REVERT: P 236 PHE cc_start: 0.6973 (t80) cc_final: 0.6466 (m-80) REVERT: P 252 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8241 (pp20) REVERT: U 24 GLN cc_start: 0.7218 (tp40) cc_final: 0.6564 (tp40) REVERT: U 28 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: A 35 GLN cc_start: 0.6385 (mm110) cc_final: 0.6083 (mm-40) REVERT: A 341 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7732 (mp) REVERT: A 370 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7028 (tp30) REVERT: A 372 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7699 (mp) REVERT: B 17 GLN cc_start: 0.7721 (tp-100) cc_final: 0.7371 (tp-100) REVERT: B 105 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8382 (t80) REVERT: B 175 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6826 (mp10) REVERT: B 280 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7399 (tmtm) REVERT: G 38 MET cc_start: 0.7228 (ttp) cc_final: 0.6873 (ttm) REVERT: G 48 ASP cc_start: 0.8503 (t0) cc_final: 0.8065 (t0) REVERT: G 50 LEU cc_start: 0.7999 (mt) cc_final: 0.7631 (mt) REVERT: G 51 LEU cc_start: 0.7609 (mp) cc_final: 0.7202 (mp) REVERT: N 32 TYR cc_start: 0.8662 (m-80) cc_final: 0.8018 (m-80) REVERT: N 115 TYR cc_start: 0.8445 (t80) cc_final: 0.8243 (t80) outliers start: 40 outliers final: 21 residues processed: 148 average time/residue: 0.5262 time to fit residues: 83.7351 Evaluate side-chains 152 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 341 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE 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 223 THR 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 280 LYS 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: 1.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 0.0970 chunk 48 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 170 GLN P 198 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.169582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135275 restraints weight = 11026.170| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.55 r_work: 0.3557 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8979 Z= 0.143 Angle : 0.509 7.028 12153 Z= 0.263 Chirality : 0.041 0.140 1352 Planarity : 0.003 0.039 1523 Dihedral : 4.868 29.322 1280 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.62 % Allowed : 18.26 % Favored : 77.12 % 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: 2.50 (0.25), residues: 424 sheet: -0.32 (0.34), residues: 216 loop : -1.02 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 288 TYR 0.014 0.001 TYR N 60 PHE 0.015 0.002 PHE P 256 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 8976) covalent geometry : angle 0.50875 / 0.26 (12147) SS BOND : bond 0.00333 / 0.17 ( 3) SS BOND : angle 0.62832 / 0.42 ( 6) hydrogen bonds : bond 0.03877 / 2.57 ( 429) hydrogen bonds : angle 3.90751 / 2.86 ( 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 180 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.338 Fit side-chains REVERT: P 234 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7792 (mt) REVERT: P 252 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7766 (pp20) REVERT: U 24 GLN cc_start: 0.7247 (tp40) cc_final: 0.6619 (tp40) REVERT: U 28 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: A 35 GLN cc_start: 0.6407 (mm110) cc_final: 0.6089 (mm-40) REVERT: A 341 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 370 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7131 (tp30) REVERT: A 372 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7723 (mp) REVERT: B 17 GLN cc_start: 0.7727 (tp-100) cc_final: 0.7355 (tp-100) REVERT: B 105 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.8416 (t80) REVERT: B 175 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6769 (mp10) REVERT: G 38 MET cc_start: 0.7337 (ttp) cc_final: 0.6961 (ttm) REVERT: G 46 LYS cc_start: 0.7172 (mptt) cc_final: 0.6909 (pttt) REVERT: G 48 ASP cc_start: 0.8588 (t0) cc_final: 0.8086 (t0) REVERT: G 50 LEU cc_start: 0.8184 (mt) cc_final: 0.7867 (mt) REVERT: G 51 LEU cc_start: 0.7776 (mp) cc_final: 0.7347 (mp) REVERT: G 52 THR cc_start: 0.7613 (m) cc_final: 0.7247 (p) REVERT: N 32 TYR cc_start: 0.8637 (m-80) cc_final: 0.7998 (m-80) REVERT: N 46 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7253 (mt-10) outliers start: 43 outliers final: 24 residues processed: 160 average time/residue: 0.5363 time to fit residues: 92.0441 Evaluate side-chains 162 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 308 ILE 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 372 ILE 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 223 THR 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 46 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4113 r_free = 0.4113 target = 0.173138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.139085 restraints weight = 10887.799| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.54 r_work: 0.3564 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8979 Z= 0.107 Angle : 0.483 8.772 12153 Z= 0.249 Chirality : 0.040 0.137 1352 Planarity : 0.003 0.039 1523 Dihedral : 4.683 31.006 1280 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.87 % Allowed : 19.33 % Favored : 76.80 % 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: 0.98 (0.26), residues: 1051 helix: 2.65 (0.25), residues: 424 sheet: -0.30 (0.34), residues: 216 loop : -0.97 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 371 TYR 0.013 0.001 TYR N 60 PHE 0.015 0.001 PHE P 358 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8976) covalent geometry : angle 0.48308 / 0.25 (12147) SS BOND : bond 0.00231 / 0.12 ( 3) SS BOND : angle 0.71863 / 0.49 ( 6) hydrogen bonds : bond 0.03488 / 2.33 ( 429) hydrogen bonds : angle 3.82800 / 2.80 ( 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 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.335 Fit side-chains REVERT: P 234 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7767 (mt) REVERT: P 236 PHE cc_start: 0.7031 (t80) cc_final: 0.6248 (m-80) REVERT: P 252 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8236 (pp20) REVERT: U 24 GLN cc_start: 0.7274 (tp40) cc_final: 0.6602 (tp-100) REVERT: U 28 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: A 35 GLN cc_start: 0.6335 (mm110) cc_final: 0.5970 (mm-40) REVERT: A 370 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7072 (tp30) REVERT: A 372 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7753 (mp) REVERT: B 14 LEU cc_start: 0.7062 (mt) cc_final: 0.6808 (mp) REVERT: B 17 GLN cc_start: 0.7745 (tp-100) cc_final: 0.7358 (tp-100) REVERT: B 55 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8713 (mt) REVERT: B 105 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8391 (t80) REVERT: B 175 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.6782 (mp10) REVERT: G 38 MET cc_start: 0.7346 (ttp) cc_final: 0.6977 (ttm) REVERT: G 46 LYS cc_start: 0.7177 (mptt) cc_final: 0.6926 (pttt) REVERT: G 48 ASP cc_start: 0.8605 (t0) cc_final: 0.8133 (t0) REVERT: G 50 LEU cc_start: 0.8107 (mt) cc_final: 0.7773 (mt) REVERT: N 32 TYR cc_start: 0.8631 (m-80) cc_final: 0.8087 (m-80) outliers start: 36 outliers final: 23 residues processed: 153 average time/residue: 0.5240 time to fit residues: 86.1774 Evaluate side-chains 156 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 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 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU 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 223 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 91 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4033 r_free = 0.4033 target = 0.167938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133733 restraints weight = 11008.446| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.55 r_work: 0.3474 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8979 Z= 0.153 Angle : 0.519 7.366 12153 Z= 0.269 Chirality : 0.041 0.142 1352 Planarity : 0.003 0.039 1523 Dihedral : 4.978 33.672 1280 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.76 % Allowed : 19.66 % Favored : 76.58 % 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: 0.87 (0.26), residues: 1051 helix: 2.54 (0.25), residues: 424 sheet: -0.36 (0.34), residues: 216 loop : -1.02 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 371 TYR 0.013 0.001 TYR N 60 PHE 0.019 0.002 PHE P 358 TRP 0.014 0.002 TRP P 377 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 8976) covalent geometry : angle 0.51877 / 0.27 (12147) SS BOND : bond 0.00282 / 0.14 ( 3) SS BOND : angle 0.71538 / 0.47 ( 6) hydrogen bonds : bond 0.03889 / 2.58 ( 429) hydrogen bonds : angle 3.94041 / 2.89 ( 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 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.337 Fit side-chains REVERT: P 185 ARG cc_start: 0.7037 (mtm180) cc_final: 0.6714 (mtm-85) REVERT: P 234 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7722 (mt) REVERT: P 252 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8245 (pp20) REVERT: U 24 GLN cc_start: 0.7193 (tp40) cc_final: 0.6598 (tp40) REVERT: U 28 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 35 GLN cc_start: 0.6210 (mm110) cc_final: 0.5887 (mm-40) REVERT: A 370 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7120 (tp30) REVERT: A 372 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7687 (mp) REVERT: B 14 LEU cc_start: 0.6970 (mt) cc_final: 0.6701 (mp) REVERT: B 17 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7289 (tp-100) REVERT: B 55 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 105 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8411 (t80) REVERT: B 175 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6649 (mp10) REVERT: G 38 MET cc_start: 0.7229 (ttp) cc_final: 0.6860 (ttm) REVERT: G 46 LYS cc_start: 0.7064 (mptt) cc_final: 0.6742 (pttt) REVERT: G 48 ASP cc_start: 0.8655 (t0) cc_final: 0.8081 (t0) REVERT: G 50 LEU cc_start: 0.8083 (mt) cc_final: 0.7761 (mt) REVERT: G 52 THR cc_start: 0.7548 (m) cc_final: 0.7198 (p) REVERT: N 32 TYR cc_start: 0.8653 (m-80) cc_final: 0.7983 (m-80) outliers start: 35 outliers final: 24 residues processed: 146 average time/residue: 0.5326 time to fit residues: 83.5947 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 55 LEU 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 223 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4047 r_free = 0.4047 target = 0.169380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135215 restraints weight = 10857.543| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.54 r_work: 0.3583 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4121 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= 0.118 Angle : 0.486 7.313 12153 Z= 0.252 Chirality : 0.040 0.138 1352 Planarity : 0.003 0.039 1523 Dihedral : 4.790 35.971 1280 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.76 % Allowed : 19.44 % Favored : 76.80 % 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: 0.99 (0.26), residues: 1051 helix: 2.67 (0.25), residues: 424 sheet: -0.30 (0.34), residues: 216 loop : -0.98 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 371 TYR 0.013 0.001 TYR N 60 PHE 0.015 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/Z covalent geometry : bond 0.00277 / 0.12 ( 8976) covalent geometry : angle 0.48588 / 0.25 (12147) SS BOND : bond 0.00229 / 0.11 ( 3) SS BOND : angle 0.68965 / 0.49 ( 6) hydrogen bonds : bond 0.03556 / 2.37 ( 429) hydrogen bonds : angle 3.84661 / 2.82 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3051.46 seconds wall clock time: 52 minutes 48.19 seconds (3168.19 seconds total)