Starting phenix.real_space_refine on Thu Mar 13 15:08:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pb1_20285/03_2025/6pb1_20285.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pb1_20285/03_2025/6pb1_20285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pb1_20285/03_2025/6pb1_20285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pb1_20285/03_2025/6pb1_20285.map" model { file = "/net/cci-nas-00/data/ceres_data/6pb1_20285/03_2025/6pb1_20285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pb1_20285/03_2025/6pb1_20285.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.72, per 1000 atoms: 0.65 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.01 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: 2.77 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2774 1.34 - 1.46: 1744 1.46 - 1.58: 4386 1.58 - 1.70: 0 1.70 - 1.81: 72 Bond restraints: 8976 Sorted by residual: bond pdb=" CA LEU P 171 " pdb=" C LEU P 171 " ideal model delta sigma weight residual 1.523 1.548 -0.024 1.30e-02 5.92e+03 3.51e+00 bond pdb=" C ILE P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 bond pdb=" CA VAL P 172 " pdb=" C VAL P 172 " ideal model delta sigma weight residual 1.522 1.543 -0.021 1.35e-02 5.49e+03 2.47e+00 bond pdb=" C5 CLR P 401 " pdb=" C6 CLR P 401 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C5 CLR P 403 " pdb=" C6 CLR P 403 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 8971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 11887 2.41 - 4.82: 228 4.82 - 7.22: 28 7.22 - 9.63: 3 9.63 - 12.04: 1 Bond angle restraints: 12147 Sorted by residual: angle pdb=" N VAL P 172 " pdb=" CA VAL P 172 " pdb=" C VAL P 172 " ideal model delta sigma weight residual 109.63 121.67 -12.04 1.44e+00 4.82e-01 6.99e+01 angle pdb=" N LEU P 171 " pdb=" CA LEU P 171 " pdb=" C LEU P 171 " ideal model delta sigma weight residual 111.28 119.28 -8.00 1.09e+00 8.42e-01 5.39e+01 angle pdb=" CA ILE P 234 " pdb=" C ILE P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 118.88 123.00 -4.12 1.54e+00 4.22e-01 7.16e+00 angle pdb=" CA PHE P 236 " pdb=" C PHE P 236 " pdb=" N PRO P 237 " ideal model delta sigma weight residual 118.44 122.67 -4.23 1.59e+00 3.96e-01 7.09e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.21 -3.81 1.45e+00 4.76e-01 6.92e+00 ... (remaining 12142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 5293 15.06 - 30.12: 173 30.12 - 45.18: 47 45.18 - 60.23: 15 60.23 - 75.29: 7 Dihedral angle restraints: 5535 sinusoidal: 2418 harmonic: 3117 Sorted by residual: dihedral pdb=" CA PRO P 235 " pdb=" C PRO P 235 " pdb=" N PHE P 236 " pdb=" CA PHE P 236 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN N 35 " pdb=" C ASN N 35 " pdb=" N TRP N 36 " pdb=" CA TRP N 36 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 5532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1216 0.084 - 0.168: 113 0.168 - 0.252: 15 0.252 - 0.336: 3 0.336 - 0.420: 5 Chirality restraints: 1352 Sorted by residual: chirality pdb=" C14 CLR P 403 " pdb=" C13 CLR P 403 " pdb=" C15 CLR P 403 " pdb=" C8 CLR P 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" C14 CLR P 401 " pdb=" C13 CLR P 401 " pdb=" C15 CLR P 401 " pdb=" C8 CLR P 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C14 CLR P 402 " pdb=" C13 CLR P 402 " pdb=" C15 CLR P 402 " pdb=" C8 CLR P 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 1349 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN P 170 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C GLN P 170 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN P 170 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU P 171 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 314 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C VAL P 314 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL P 314 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU P 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 301 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C VAL A 301 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 301 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 302 " 0.015 2.00e-02 2.50e+03 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2334 2.81 - 3.33: 7328 3.33 - 3.86: 13870 3.86 - 4.38: 16228 4.38 - 4.90: 28550 Nonbonded interactions: 68310 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.335 3.040 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.346 3.120 nonbonded pdb=" OG SER P 297 " pdb=" NH1 ARG A 385 " model vdw 2.371 3.120 ... (remaining 68305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 24.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8976 Z= 0.222 Angle : 0.788 12.041 12147 Z= 0.421 Chirality : 0.059 0.420 1352 Planarity : 0.006 0.063 1523 Dihedral : 9.366 75.292 3506 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (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 TRP 0.031 0.003 TRP B 169 HIS 0.016 0.002 HIS A 220 PHE 0.026 0.002 PHE P 327 TYR 0.026 0.002 TYR N 115 ARG 0.007 0.000 ARG N 118 *********************** 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 : 0.943 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: 1.1900 time to fit residues: 304.7926 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 : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 152 HIS P 304 GLN P 351 GLN P 381 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 387 HIS B 88 ASN B 266 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142447 restraints weight = 10783.295| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.59 r_work: 0.3597 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8976 Z= 0.199 Angle : 0.538 7.580 12147 Z= 0.276 Chirality : 0.041 0.143 1352 Planarity : 0.004 0.042 1523 Dihedral : 7.193 59.911 1504 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.51 % Allowed : 10.96 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1051 helix: 0.83 (0.24), residues: 434 sheet: -1.10 (0.31), residues: 219 loop : -1.85 (0.26), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE P 358 TYR 0.014 0.001 TYR A 37 ARG 0.003 0.000 ARG P 185 *********************** 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 203 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.957 Fit side-chains REVERT: P 109 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.5737 (p90) REVERT: P 234 ILE cc_start: 0.7651 (mt) cc_final: 0.7213 (mt) REVERT: P 236 PHE cc_start: 0.6837 (t80) cc_final: 0.6289 (m-80) REVERT: U 24 GLN cc_start: 0.7175 (tp40) cc_final: 0.6520 (tp-100) REVERT: U 28 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: A 209 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7663 (pt0) REVERT: A 221 MET cc_start: 0.8042 (ttm) cc_final: 0.7500 (tpp) REVERT: A 310 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7002 (p0) REVERT: A 341 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7724 (mp) REVERT: A 370 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6814 (tp30) REVERT: B 17 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7369 (tp-100) REVERT: B 55 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8691 (mt) REVERT: B 96 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6746 (ptp-170) REVERT: B 134 ARG cc_start: 0.5774 (mmm-85) cc_final: 0.5519 (mmm160) REVERT: B 188 MET cc_start: 0.8715 (mmm) cc_final: 0.8468 (mmt) REVERT: B 234 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7482 (m-80) outliers start: 42 outliers final: 15 residues processed: 180 average time/residue: 1.2240 time to fit residues: 235.6918 Evaluate side-chains 161 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain U residue 4 SER Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 310 ASP 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 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 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 15 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 84 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 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 = 0.4083 r_free = 0.4083 target = 0.171999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137411 restraints weight = 10980.225| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.57 r_work: 0.3507 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8976 Z= 0.225 Angle : 0.517 6.423 12147 Z= 0.269 Chirality : 0.041 0.134 1352 Planarity : 0.003 0.040 1523 Dihedral : 7.374 59.731 1504 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.83 % Allowed : 13.00 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1051 helix: 1.62 (0.25), residues: 434 sheet: -0.76 (0.32), residues: 208 loop : -1.67 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.002 PHE A 212 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG P 373 *********************** 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 194 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.882 Fit side-chains REVERT: P 109 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.6234 (p90) REVERT: P 170 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.6509 (mp-120) REVERT: P 234 ILE cc_start: 0.7920 (mt) cc_final: 0.7544 (mt) REVERT: P 236 PHE cc_start: 0.6844 (t80) cc_final: 0.6027 (m-80) REVERT: P 302 THR cc_start: 0.6926 (m) cc_final: 0.6712 (p) REVERT: P 348 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: U 24 GLN cc_start: 0.7129 (tp40) cc_final: 0.6535 (tp40) REVERT: U 28 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: A 370 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7013 (tm-30) REVERT: A 372 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7663 (mp) REVERT: B 17 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7302 (tp-100) REVERT: B 55 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8689 (mt) REVERT: B 96 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6746 (ptp-170) REVERT: B 105 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8384 (t80) REVERT: B 175 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6695 (mp10) REVERT: B 188 MET cc_start: 0.8655 (mmm) cc_final: 0.8453 (mmt) REVERT: B 214 ARG cc_start: 0.7446 (mmt180) cc_final: 0.7181 (mmt180) REVERT: B 234 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: B 259 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: B 280 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7650 (tmtm) REVERT: G 38 MET cc_start: 0.7273 (ttp) cc_final: 0.6877 (ttm) outliers start: 45 outliers final: 23 residues processed: 171 average time/residue: 1.0336 time to fit residues: 190.4622 Evaluate side-chains 166 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 170 GLN Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 348 GLN 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 310 ASP 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 59 TYR 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 175 GLN Chi-restraints excluded: chain B residue 191 SER 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 280 LYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 43 LYS 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 39 optimal weight: 0.0040 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140072 restraints weight = 10776.868| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.52 r_work: 0.3568 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8976 Z= 0.142 Angle : 0.468 7.056 12147 Z= 0.243 Chirality : 0.040 0.131 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.980 58.704 1504 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.19 % Allowed : 15.57 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1051 helix: 2.04 (0.25), residues: 431 sheet: -0.70 (0.32), residues: 213 loop : -1.40 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE P 256 TYR 0.013 0.001 TYR A 37 ARG 0.008 0.000 ARG P 288 *********************** 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: 39 poor density : 146 time to evaluate : 0.917 Fit side-chains REVERT: P 109 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.6055 (p90) REVERT: P 234 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7726 (mt) REVERT: P 236 PHE cc_start: 0.6894 (t80) cc_final: 0.6346 (m-80) REVERT: P 252 GLU cc_start: 0.8339 (pp20) cc_final: 0.8091 (pp20) REVERT: P 348 GLN cc_start: 0.7830 (tt0) cc_final: 0.7605 (tm-30) REVERT: U 24 GLN cc_start: 0.7208 (tp40) cc_final: 0.6494 (tp-100) REVERT: U 28 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: A 27 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7225 (mt-10) REVERT: A 300 LYS cc_start: 0.5990 (mmtt) cc_final: 0.5723 (tttt) REVERT: A 370 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7071 (tm-30) REVERT: A 372 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7820 (mp) REVERT: B 17 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7396 (tp-100) REVERT: B 55 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8731 (mt) REVERT: B 105 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8367 (t80) REVERT: B 175 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6744 (mp10) REVERT: B 234 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: B 259 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: G 38 MET cc_start: 0.7325 (ttp) cc_final: 0.6944 (ttm) outliers start: 39 outliers final: 20 residues processed: 165 average time/residue: 1.1991 time to fit residues: 213.4332 Evaluate side-chains 158 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 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 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 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 59 SER Chi-restraints excluded: chain N residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 31 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN U 33 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.172998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138825 restraints weight = 10797.338| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.53 r_work: 0.3552 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8976 Z= 0.169 Angle : 0.477 7.280 12147 Z= 0.248 Chirality : 0.040 0.140 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.833 59.545 1504 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.94 % Allowed : 15.57 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1051 helix: 2.22 (0.25), residues: 431 sheet: -0.59 (0.33), residues: 215 loop : -1.26 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE P 256 TYR 0.015 0.001 TYR N 60 ARG 0.007 0.000 ARG P 288 *********************** 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 189 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 0.883 Fit side-chains REVERT: P 109 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.6213 (p90) REVERT: P 220 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6308 (pm20) REVERT: P 234 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7679 (mt) REVERT: P 236 PHE cc_start: 0.6880 (t80) cc_final: 0.6347 (m-80) REVERT: P 252 GLU cc_start: 0.8354 (pp20) cc_final: 0.7804 (pp20) REVERT: P 348 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: U 24 GLN cc_start: 0.7175 (tp40) cc_final: 0.6537 (tp40) REVERT: U 28 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: A 27 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 300 LYS cc_start: 0.5990 (mmtt) cc_final: 0.5754 (pttp) REVERT: A 370 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7015 (tp30) REVERT: A 372 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 17 GLN cc_start: 0.7701 (tp-100) cc_final: 0.7351 (tp-100) REVERT: B 55 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8702 (mt) REVERT: B 105 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8386 (t80) REVERT: B 134 ARG cc_start: 0.6493 (mmm160) cc_final: 0.6177 (mmm160) REVERT: B 175 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: B 214 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7414 (mmt180) REVERT: B 234 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: B 259 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.6803 (pm20) REVERT: G 38 MET cc_start: 0.7251 (ttp) cc_final: 0.6880 (ttm) outliers start: 46 outliers final: 23 residues processed: 164 average time/residue: 1.2232 time to fit residues: 215.2047 Evaluate side-chains 167 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 234 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 348 GLN 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 372 ILE 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 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 Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137846 restraints weight = 10798.738| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.55 r_work: 0.3561 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8976 Z= 0.144 Angle : 0.467 7.926 12147 Z= 0.242 Chirality : 0.040 0.139 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.580 57.911 1504 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.40 % Allowed : 16.22 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1051 helix: 2.35 (0.25), residues: 431 sheet: -0.49 (0.33), residues: 215 loop : -1.13 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 357 PHE 0.016 0.001 PHE P 256 TYR 0.016 0.001 TYR N 60 ARG 0.005 0.000 ARG P 288 *********************** 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 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.942 Fit side-chains REVERT: P 170 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.6214 (mp-120) REVERT: P 220 GLU cc_start: 0.6470 (mm-30) cc_final: 0.6261 (pm20) REVERT: P 234 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7693 (mt) REVERT: P 236 PHE cc_start: 0.6916 (t80) cc_final: 0.6371 (m-80) REVERT: P 252 GLU cc_start: 0.8426 (pp20) cc_final: 0.7792 (pp20) REVERT: P 348 GLN cc_start: 0.7884 (tt0) cc_final: 0.7678 (tm-30) REVERT: U 24 GLN cc_start: 0.7175 (tp40) cc_final: 0.6548 (tp40) REVERT: U 28 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: A 300 LYS cc_start: 0.6054 (mmtt) cc_final: 0.5813 (tttt) REVERT: A 370 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6992 (tp30) REVERT: A 372 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7622 (mp) REVERT: B 17 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7303 (tp-100) REVERT: B 55 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8713 (mt) REVERT: B 105 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 175 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: B 259 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: G 38 MET cc_start: 0.7213 (ttp) cc_final: 0.6854 (ttm) REVERT: N 32 TYR cc_start: 0.8659 (m-80) cc_final: 0.8000 (m-80) REVERT: N 82 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6309 (tp40) outliers start: 41 outliers final: 24 residues processed: 157 average time/residue: 1.3508 time to fit residues: 227.6577 Evaluate side-chains 159 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 372 ILE 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 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 28 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 6.9990 chunk 50 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN P 351 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.175738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141899 restraints weight = 10851.997| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.52 r_work: 0.3636 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8976 Z= 0.171 Angle : 0.472 7.084 12147 Z= 0.246 Chirality : 0.040 0.140 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.515 56.687 1504 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.83 % Allowed : 16.76 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1051 helix: 2.41 (0.25), residues: 431 sheet: -0.45 (0.33), residues: 215 loop : -1.07 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.001 PHE P 256 TYR 0.016 0.001 TYR N 60 ARG 0.005 0.000 ARG P 288 *********************** 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 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.868 Fit side-chains REVERT: P 220 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6336 (pm20) REVERT: P 234 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7744 (mt) REVERT: P 236 PHE cc_start: 0.7022 (t80) cc_final: 0.6540 (m-80) REVERT: P 252 GLU cc_start: 0.8434 (pp20) cc_final: 0.8205 (pp20) REVERT: P 348 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: U 24 GLN cc_start: 0.7249 (tp40) cc_final: 0.6581 (tp40) REVERT: U 28 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6656 (mp0) REVERT: A 300 LYS cc_start: 0.6233 (mmtt) cc_final: 0.6002 (tttt) REVERT: A 370 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7106 (tp30) REVERT: A 372 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7699 (mp) REVERT: B 17 GLN cc_start: 0.7760 (tp-100) cc_final: 0.7409 (tp-100) REVERT: B 55 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 105 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8381 (t80) REVERT: B 175 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6862 (mp10) REVERT: B 280 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7491 (tmtm) REVERT: G 38 MET cc_start: 0.7397 (ttp) cc_final: 0.7025 (ttm) REVERT: G 48 ASP cc_start: 0.8566 (t0) cc_final: 0.8302 (t0) REVERT: N 32 TYR cc_start: 0.8614 (m-80) cc_final: 0.8051 (m-80) REVERT: N 43 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6819 (ttmt) REVERT: N 82 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6429 (tp40) outliers start: 45 outliers final: 25 residues processed: 156 average time/residue: 1.1573 time to fit residues: 193.5691 Evaluate side-chains 164 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain P residue 348 GLN 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 372 ILE 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 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 GLN 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 28 THR Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.179390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.146014 restraints weight = 10872.207| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.53 r_work: 0.3584 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8976 Z= 0.136 Angle : 0.460 7.164 12147 Z= 0.239 Chirality : 0.039 0.136 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.291 56.712 1504 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.19 % Allowed : 17.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1051 helix: 2.56 (0.25), residues: 431 sheet: -0.36 (0.34), residues: 216 loop : -1.01 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.016 0.001 PHE P 256 TYR 0.015 0.001 TYR N 60 ARG 0.007 0.000 ARG P 371 *********************** 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 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 1.063 Fit side-chains REVERT: P 220 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6294 (pm20) REVERT: P 234 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7675 (mt) REVERT: P 236 PHE cc_start: 0.6973 (t80) cc_final: 0.6480 (m-80) REVERT: P 252 GLU cc_start: 0.8433 (pp20) cc_final: 0.8173 (pp20) REVERT: P 348 GLN cc_start: 0.7999 (tt0) cc_final: 0.7750 (tm-30) REVERT: U 24 GLN cc_start: 0.7278 (tp40) cc_final: 0.6651 (tp40) REVERT: U 28 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: A 341 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7759 (mp) REVERT: A 370 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7037 (tp30) REVERT: A 372 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7664 (mp) REVERT: B 17 GLN cc_start: 0.7722 (tp-100) cc_final: 0.7372 (tp-100) REVERT: B 105 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8385 (t80) REVERT: B 175 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6839 (mp10) REVERT: B 280 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7543 (tmtm) REVERT: G 38 MET cc_start: 0.7401 (ttp) cc_final: 0.7028 (ttm) REVERT: G 48 ASP cc_start: 0.8592 (t0) cc_final: 0.8284 (t0) REVERT: N 32 TYR cc_start: 0.8596 (m-80) cc_final: 0.8026 (m-80) outliers start: 39 outliers final: 24 residues processed: 157 average time/residue: 1.1822 time to fit residues: 199.4010 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 : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 168 LEU 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 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 59 TYR 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 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 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN ** A 59 GLN ** 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 = 0.4061 r_free = 0.4061 target = 0.169995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135897 restraints weight = 11010.158| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.54 r_work: 0.3515 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8976 Z= 0.221 Angle : 0.520 8.827 12147 Z= 0.269 Chirality : 0.041 0.140 1352 Planarity : 0.003 0.038 1523 Dihedral : 6.601 54.944 1504 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.30 % Allowed : 18.37 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1051 helix: 2.44 (0.25), residues: 431 sheet: -0.38 (0.33), residues: 216 loop : -1.00 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.002 PHE P 256 TYR 0.020 0.001 TYR N 60 ARG 0.008 0.000 ARG P 288 *********************** 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 174 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.959 Fit side-chains REVERT: P 220 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6318 (pm20) REVERT: P 234 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7723 (mt) REVERT: P 252 GLU cc_start: 0.8452 (pp20) cc_final: 0.8237 (pp20) REVERT: P 348 GLN cc_start: 0.8014 (tt0) cc_final: 0.7706 (tm-30) REVERT: U 24 GLN cc_start: 0.7179 (tp40) cc_final: 0.6586 (tp40) REVERT: U 28 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 341 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7686 (mp) REVERT: A 370 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7099 (tp30) REVERT: A 372 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 17 GLN cc_start: 0.7688 (tp-100) cc_final: 0.7315 (tp-100) REVERT: B 105 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8426 (t80) REVERT: B 175 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6684 (mp10) REVERT: B 280 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7274 (tmtm) REVERT: G 38 MET cc_start: 0.7230 (ttp) cc_final: 0.6848 (ttm) REVERT: G 48 ASP cc_start: 0.8624 (t0) cc_final: 0.8307 (t0) REVERT: G 50 LEU cc_start: 0.8007 (mt) cc_final: 0.7664 (mt) REVERT: N 32 TYR cc_start: 0.8577 (m-80) cc_final: 0.7910 (m-80) outliers start: 40 outliers final: 25 residues processed: 154 average time/residue: 1.0787 time to fit residues: 178.5764 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR 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 G residue 51 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 68 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.169194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135289 restraints weight = 10958.450| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.51 r_work: 0.3538 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8976 Z= 0.195 Angle : 0.501 7.308 12147 Z= 0.261 Chirality : 0.041 0.140 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.496 54.933 1504 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.65 % Allowed : 19.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1051 helix: 2.50 (0.25), residues: 431 sheet: -0.39 (0.33), residues: 216 loop : -1.00 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE P 358 TYR 0.020 0.001 TYR N 60 ARG 0.009 0.000 ARG P 288 ********************** 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: 34 poor density : 129 time to evaluate : 0.877 Fit side-chains REVERT: P 220 GLU cc_start: 0.6588 (mm-30) cc_final: 0.6320 (pm20) REVERT: P 234 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7740 (mt) REVERT: P 252 GLU cc_start: 0.8504 (pp20) cc_final: 0.8297 (pp20) REVERT: P 348 GLN cc_start: 0.8059 (tt0) cc_final: 0.7760 (tm-30) REVERT: U 24 GLN cc_start: 0.7199 (tp40) cc_final: 0.6529 (tp-100) REVERT: U 28 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: A 370 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7172 (tp30) REVERT: A 372 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7728 (mp) REVERT: B 17 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7304 (tp-100) REVERT: B 105 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8399 (t80) REVERT: B 175 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6678 (mp10) REVERT: G 38 MET cc_start: 0.7195 (ttp) cc_final: 0.6844 (ttm) REVERT: G 51 LEU cc_start: 0.7555 (tt) cc_final: 0.7270 (mp) REVERT: N 32 TYR cc_start: 0.8607 (m-80) cc_final: 0.8085 (m-80) REVERT: N 43 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6452 (mtpm) outliers start: 34 outliers final: 24 residues processed: 148 average time/residue: 1.0843 time to fit residues: 172.3074 Evaluate side-chains 157 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 168 LEU 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 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR 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 28 THR Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 65 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN P 174 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.175332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142064 restraints weight = 10870.265| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.45 r_work: 0.3592 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8976 Z= 0.139 Angle : 0.483 11.624 12147 Z= 0.248 Chirality : 0.040 0.137 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.180 56.783 1504 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.33 % Allowed : 19.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1051 helix: 2.66 (0.25), residues: 431 sheet: -0.37 (0.34), residues: 216 loop : -0.92 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.016 0.001 PHE P 256 TYR 0.019 0.001 TYR N 60 ARG 0.009 0.000 ARG P 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6315.10 seconds wall clock time: 111 minutes 30.71 seconds (6690.71 seconds total)