Starting phenix.real_space_refine on Thu Feb 13 12:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pb1_20285/02_2025/6pb1_20285.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pb1_20285/02_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_20285/02_2025/6pb1_20285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pb1_20285/02_2025/6pb1_20285.map" model { file = "/net/cci-nas-00/data/ceres_data/6pb1_20285/02_2025/6pb1_20285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pb1_20285/02_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-5592/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: 5.26, per 1000 atoms: 0.60 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: 2.23 Conformation dependent library (CDL) restraints added in 920.1 milliseconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 42.7% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 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: 2.22 Time building geometry restraints manager: 2.57 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: 0.640 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.090 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- 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 : 0.929 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: 1.2449 time to fit residues: 318.5658 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 : 1.019 ------------------------------------------------------------------------------- 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 = 0.176851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.142455 restraints weight = 10782.955| |-----------------------------------------------------------------------------| r_work (start): 0.3711 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: 0.7121 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 : 5.91 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 : 0.896 Fit side-chains REVERT: P 109 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.5736 (p90) REVERT: P 234 ILE cc_start: 0.7650 (mt) cc_final: 0.7212 (mt) REVERT: P 236 PHE cc_start: 0.6836 (t80) cc_final: 0.6289 (m-80) REVERT: U 24 GLN cc_start: 0.7178 (tp40) cc_final: 0.6523 (tp-100) REVERT: U 28 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: A 209 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7662 (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: 0.7003 (p0) REVERT: A 341 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7725 (mp) REVERT: A 370 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6812 (tp30) REVERT: B 17 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7370 (tp-100) REVERT: B 55 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8690 (mt) REVERT: B 96 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6748 (ptp-170) REVERT: B 134 ARG cc_start: 0.5772 (mmm-85) cc_final: 0.5517 (mmm160) REVERT: B 188 MET cc_start: 0.8715 (mmm) cc_final: 0.8468 (mmt) REVERT: B 234 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7481 (m-80) outliers start: 42 outliers final: 15 residues processed: 180 average time/residue: 1.1831 time to fit residues: 227.5595 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 : 0.897 ------------------------------------------------------------------------------- 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: 10.0000 chunk 12 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 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** N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.172049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137356 restraints weight = 10978.571| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.57 r_work: 0.3507 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3188 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= 0.220 Angle : 0.516 6.426 12147 Z= 0.269 Chirality : 0.041 0.139 1352 Planarity : 0.003 0.040 1523 Dihedral : 7.369 59.907 1504 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.73 % Allowed : 13.00 % Favored : 82.28 % 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: -0.19 (0.25), residues: 1051 helix: 1.60 (0.25), residues: 434 sheet: -0.80 (0.32), residues: 209 loop : -1.67 (0.26), residues: 408 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 0.013 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 192 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.918 Fit side-chains REVERT: P 109 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.6233 (p90) REVERT: P 170 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.6507 (mp-120) REVERT: P 234 ILE cc_start: 0.7916 (mt) cc_final: 0.7543 (mt) REVERT: P 236 PHE cc_start: 0.6838 (t80) cc_final: 0.6027 (m-80) REVERT: P 302 THR cc_start: 0.6928 (m) cc_final: 0.6714 (p) REVERT: U 24 GLN cc_start: 0.7133 (tp40) cc_final: 0.6537 (tp40) REVERT: U 28 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: A 209 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7754 (pt0) REVERT: A 370 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7020 (tm-30) REVERT: A 372 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7663 (mp) REVERT: B 17 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7307 (tp-100) REVERT: B 55 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8692 (mt) REVERT: B 96 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6743 (ptp-170) REVERT: B 105 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8387 (t80) REVERT: B 175 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.6694 (mp10) REVERT: B 188 MET cc_start: 0.8658 (mmm) cc_final: 0.8455 (mmt) REVERT: B 214 ARG cc_start: 0.7446 (mmt180) cc_final: 0.7184 (mmt180) REVERT: B 234 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: B 259 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: B 280 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7582 (tmtm) REVERT: G 38 MET cc_start: 0.7277 (ttp) cc_final: 0.6883 (ttm) outliers start: 44 outliers final: 23 residues processed: 169 average time/residue: 1.0856 time to fit residues: 197.2250 Evaluate side-chains 165 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 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 96 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 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: 0.6980 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 33 ASN ** 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 = 0.4056 r_free = 0.4056 target = 0.169134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135136 restraints weight = 10892.382| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.51 r_work: 0.3492 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8976 Z= 0.273 Angle : 0.540 6.179 12147 Z= 0.281 Chirality : 0.042 0.134 1352 Planarity : 0.004 0.040 1523 Dihedral : 7.375 56.485 1504 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.26 % Allowed : 14.61 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.08 (0.25), residues: 1051 helix: 1.85 (0.25), residues: 427 sheet: -0.67 (0.33), residues: 208 loop : -1.48 (0.27), residues: 416 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 0.015 0.002 PHE P 256 TYR 0.013 0.001 TYR P 249 ARG 0.009 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 191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 142 time to evaluate : 1.166 Fit side-chains REVERT: P 109 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6296 (p90) REVERT: P 220 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6307 (pm20) REVERT: P 234 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7920 (mt) REVERT: U 24 GLN cc_start: 0.7158 (tp40) cc_final: 0.6535 (tp40) REVERT: U 28 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6357 (mp0) REVERT: A 209 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7974 (pt0) REVERT: A 300 LYS cc_start: 0.6063 (mmtt) cc_final: 0.5781 (pttp) REVERT: A 370 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7148 (tm-30) REVERT: A 372 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7807 (mp) REVERT: B 17 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7304 (tp-100) REVERT: B 55 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 96 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6545 (ptp-170) REVERT: B 105 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8491 (t80) REVERT: B 175 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6588 (mp10) REVERT: B 234 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: G 38 MET cc_start: 0.7314 (ttp) cc_final: 0.6937 (ttm) REVERT: N 43 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6272 (mtpp) REVERT: N 115 TYR cc_start: 0.8612 (t80) cc_final: 0.8364 (t80) outliers start: 49 outliers final: 27 residues processed: 165 average time/residue: 1.0948 time to fit residues: 194.3969 Evaluate side-chains 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 215 MET Chi-restraints excluded: chain P residue 234 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 4 SER Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 310 ASP 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 96 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 31 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.169547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135200 restraints weight = 10836.590| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.53 r_work: 0.3499 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8976 Z= 0.214 Angle : 0.509 7.329 12147 Z= 0.264 Chirality : 0.041 0.141 1352 Planarity : 0.003 0.039 1523 Dihedral : 7.031 54.893 1504 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.83 % Allowed : 15.36 % Favored : 79.81 % 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: 0.36 (0.25), residues: 1051 helix: 2.11 (0.25), residues: 424 sheet: -0.48 (0.34), residues: 208 loop : -1.37 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE P 256 TYR 0.016 0.001 TYR N 60 ARG 0.008 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 191 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 1.040 Fit side-chains REVERT: P 109 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.6334 (p90) REVERT: P 170 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7958 (tp40) REVERT: P 220 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6299 (pm20) REVERT: P 244 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7617 (mp) REVERT: U 24 GLN cc_start: 0.7114 (tp40) cc_final: 0.6475 (tp40) REVERT: U 28 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: A 300 LYS cc_start: 0.6207 (mmtt) cc_final: 0.5927 (tttt) REVERT: A 370 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7188 (tp30) REVERT: A 372 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7766 (mp) REVERT: B 17 GLN cc_start: 0.7705 (tp-100) cc_final: 0.7310 (tp-100) REVERT: B 55 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8706 (mt) REVERT: B 105 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 175 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: B 234 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: G 38 MET cc_start: 0.7337 (ttp) cc_final: 0.6948 (ttm) REVERT: N 115 TYR cc_start: 0.8518 (t80) cc_final: 0.8229 (t80) outliers start: 45 outliers final: 22 residues processed: 167 average time/residue: 1.1374 time to fit residues: 203.7834 Evaluate side-chains 167 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 244 ILE Chi-restraints excluded: chain P residue 303 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.170342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136310 restraints weight = 10835.556| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.53 r_work: 0.3525 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3788 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= 0.153 Angle : 0.474 6.841 12147 Z= 0.247 Chirality : 0.040 0.139 1352 Planarity : 0.003 0.039 1523 Dihedral : 6.664 56.607 1504 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.30 % Allowed : 16.11 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.26), residues: 1051 helix: 2.38 (0.25), residues: 424 sheet: -0.51 (0.34), residues: 214 loop : -1.20 (0.28), residues: 413 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 0.017 0.001 PHE P 256 TYR 0.012 0.001 TYR A 37 ARG 0.006 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 178 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.920 Fit side-chains REVERT: P 185 ARG cc_start: 0.6827 (mtt180) cc_final: 0.6619 (mtm-85) REVERT: P 202 MET cc_start: 0.8336 (mtt) cc_final: 0.8081 (mtm) REVERT: P 220 GLU cc_start: 0.6526 (mm-30) cc_final: 0.6278 (pm20) REVERT: P 236 PHE cc_start: 0.7016 (t80) cc_final: 0.6133 (m-80) REVERT: U 24 GLN cc_start: 0.7136 (tp40) cc_final: 0.6493 (tp40) REVERT: U 28 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: A 300 LYS cc_start: 0.6185 (mmtt) cc_final: 0.5917 (tttt) REVERT: A 341 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7667 (mp) REVERT: A 370 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7159 (tp30) REVERT: A 372 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7751 (mp) REVERT: B 17 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7329 (tp-100) REVERT: B 55 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8707 (mt) REVERT: B 105 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8377 (t80) REVERT: B 134 ARG cc_start: 0.6488 (mmm160) cc_final: 0.6190 (mmm160) REVERT: B 175 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6675 (mp10) REVERT: B 259 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6850 (pm20) REVERT: G 38 MET cc_start: 0.7210 (ttp) cc_final: 0.6829 (ttm) REVERT: G 48 ASP cc_start: 0.8562 (t0) cc_final: 0.8145 (t0) REVERT: N 32 TYR cc_start: 0.8665 (m-80) cc_final: 0.8069 (m-80) REVERT: N 43 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6704 (mtmt) REVERT: N 115 TYR cc_start: 0.8528 (t80) cc_final: 0.8236 (t80) outliers start: 40 outliers final: 22 residues processed: 161 average time/residue: 1.1734 time to fit residues: 202.3220 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 145 ARG Chi-restraints excluded: chain P residue 164 VAL Chi-restraints excluded: chain P residue 168 LEU 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 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 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 46 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3992 r_free = 0.3992 target = 0.163145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129754 restraints weight = 11126.012| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.49 r_work: 0.3439 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8976 Z= 0.467 Angle : 0.666 8.103 12147 Z= 0.346 Chirality : 0.048 0.191 1352 Planarity : 0.005 0.040 1523 Dihedral : 7.883 59.980 1504 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.59 % Allowed : 16.33 % Favored : 78.09 % 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: 0.10 (0.25), residues: 1051 helix: 1.83 (0.24), residues: 424 sheet: -0.67 (0.34), residues: 212 loop : -1.40 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP P 377 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.003 PHE P 194 TYR 0.016 0.002 TYR P 249 ARG 0.006 0.001 ARG P 371 *********************** 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 185 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 1.021 Fit side-chains REVERT: P 220 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6338 (pm20) REVERT: U 24 GLN cc_start: 0.7237 (tp40) cc_final: 0.6577 (tp40) REVERT: U 28 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: A 283 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7426 (mtm180) REVERT: A 300 LYS cc_start: 0.6140 (mmtt) cc_final: 0.5864 (tttt) REVERT: A 370 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7675 (tt0) REVERT: A 372 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 390 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: B 17 GLN cc_start: 0.7643 (tp-100) cc_final: 0.7140 (tp-100) REVERT: B 55 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8785 (mt) REVERT: B 96 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6626 (ptp-170) REVERT: B 105 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8478 (t80) REVERT: B 134 ARG cc_start: 0.6699 (mmm160) cc_final: 0.6380 (mmm160) REVERT: B 175 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: B 234 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: G 38 MET cc_start: 0.7328 (ttp) cc_final: 0.7093 (ttp) REVERT: G 52 THR cc_start: 0.7791 (m) cc_final: 0.7424 (p) REVERT: N 5 GLN cc_start: 0.6809 (tp-100) cc_final: 0.6581 (tt0) REVERT: N 46 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6855 (tt0) outliers start: 52 outliers final: 32 residues processed: 164 average time/residue: 1.2113 time to fit residues: 212.2672 Evaluate side-chains 171 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 4 SER Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 ASP 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 390 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 173 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 273 ILE 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 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 GLU 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 Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 174 HIS P 198 ASN ** 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 = 0.4034 r_free = 0.4034 target = 0.168696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134598 restraints weight = 11125.181| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.55 r_work: 0.3489 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4151 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= 0.151 Angle : 0.501 7.231 12147 Z= 0.261 Chirality : 0.040 0.140 1352 Planarity : 0.003 0.040 1523 Dihedral : 6.761 56.305 1504 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.08 % Allowed : 18.58 % 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: 0.57 (0.26), residues: 1051 helix: 2.35 (0.25), residues: 424 sheet: -0.48 (0.34), residues: 208 loop : -1.27 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE P 256 TYR 0.014 0.001 TYR N 115 ARG 0.005 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 176 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.940 Fit side-chains REVERT: P 220 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6300 (pm20) REVERT: U 24 GLN cc_start: 0.7217 (tp40) cc_final: 0.6563 (tp40) REVERT: U 28 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6540 (mp0) REVERT: A 300 LYS cc_start: 0.6150 (mmtt) cc_final: 0.5893 (tttt) REVERT: A 370 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7587 (tt0) REVERT: A 372 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7706 (mp) REVERT: B 14 LEU cc_start: 0.6980 (mt) cc_final: 0.6725 (mp) REVERT: B 17 GLN cc_start: 0.7655 (tp-100) cc_final: 0.7215 (tp-100) REVERT: B 55 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8752 (mt) REVERT: B 105 TYR cc_start: 0.8919 (OUTLIER) cc_final: 0.8301 (t80) REVERT: B 134 ARG cc_start: 0.6515 (mmm160) cc_final: 0.6245 (mmm160) REVERT: B 175 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: B 214 ARG cc_start: 0.7840 (mmt180) cc_final: 0.7617 (mpt-90) REVERT: G 38 MET cc_start: 0.7244 (ttp) cc_final: 0.6880 (ttm) REVERT: N 32 TYR cc_start: 0.8627 (m-80) cc_final: 0.8114 (m-80) REVERT: N 46 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: N 82 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6349 (tp40) REVERT: N 115 TYR cc_start: 0.8411 (t80) cc_final: 0.8142 (t80) outliers start: 38 outliers final: 24 residues processed: 160 average time/residue: 1.1320 time to fit residues: 194.2593 Evaluate side-chains 160 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 164 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain 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 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 46 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 82 optimal weight: 0.0770 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.0010 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 30.0000 overall best weight: 0.6548 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.170973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.137133 restraints weight = 10996.425| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.54 r_work: 0.3507 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8976 Z= 0.142 Angle : 0.488 9.009 12147 Z= 0.253 Chirality : 0.040 0.138 1352 Planarity : 0.003 0.041 1523 Dihedral : 6.314 59.878 1504 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.19 % Allowed : 18.90 % Favored : 76.91 % 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: 0.86 (0.26), residues: 1051 helix: 2.61 (0.25), residues: 424 sheet: -0.48 (0.33), residues: 215 loop : -1.05 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.020 0.001 PHE P 256 TYR 0.016 0.001 TYR N 115 ARG 0.007 0.000 ARG P 371 *********************** 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 181 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.970 Fit side-chains REVERT: P 170 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6255 (mp-120) REVERT: P 220 GLU cc_start: 0.6515 (mm-30) cc_final: 0.6297 (pm20) REVERT: P 236 PHE cc_start: 0.6998 (t80) cc_final: 0.6066 (m-80) REVERT: U 24 GLN cc_start: 0.7253 (tp40) cc_final: 0.6574 (tp40) REVERT: U 28 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: A 221 MET cc_start: 0.8044 (ttm) cc_final: 0.7503 (tpp) REVERT: A 370 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7184 (tp30) REVERT: A 372 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 14 LEU cc_start: 0.6963 (mt) cc_final: 0.6706 (mp) REVERT: B 17 GLN cc_start: 0.7669 (tp-100) cc_final: 0.7257 (tp-100) REVERT: B 55 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8771 (mt) REVERT: B 175 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6671 (mp10) REVERT: B 197 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7352 (mmm-85) REVERT: B 214 ARG cc_start: 0.7822 (mmt180) cc_final: 0.7556 (mpt-90) REVERT: G 38 MET cc_start: 0.7055 (ttp) cc_final: 0.6700 (ttm) REVERT: N 32 TYR cc_start: 0.8523 (m-80) cc_final: 0.8040 (m-80) REVERT: N 115 TYR cc_start: 0.8330 (t80) cc_final: 0.8093 (t80) REVERT: N 117 TYR cc_start: 0.7960 (m-10) cc_final: 0.7716 (m-80) outliers start: 39 outliers final: 27 residues processed: 165 average time/residue: 1.0958 time to fit residues: 194.4241 Evaluate side-chains 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 170 GLN Chi-restraints excluded: chain P residue 247 LEU 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 143 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.169555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.135848 restraints weight = 10937.382| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.52 r_work: 0.3519 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8976 Z= 0.171 Angle : 0.503 8.011 12147 Z= 0.261 Chirality : 0.040 0.139 1352 Planarity : 0.003 0.040 1523 Dihedral : 6.314 57.947 1504 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.33 % Allowed : 19.98 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.26), residues: 1051 helix: 2.65 (0.25), residues: 424 sheet: -0.46 (0.33), residues: 215 loop : -1.01 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE P 256 TYR 0.015 0.001 TYR B 124 ARG 0.008 0.000 ARG P 371 ********************** 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 168 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.868 Fit side-chains REVERT: P 170 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6167 (mp-120) REVERT: P 202 MET cc_start: 0.8335 (mtt) cc_final: 0.8076 (mtm) REVERT: P 220 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6284 (pm20) REVERT: U 24 GLN cc_start: 0.7303 (tp40) cc_final: 0.6680 (tp40) REVERT: U 28 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: A 221 MET cc_start: 0.8046 (ttm) cc_final: 0.7505 (tpp) REVERT: A 370 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7164 (tp30) REVERT: A 372 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7626 (mp) REVERT: B 14 LEU cc_start: 0.6989 (mt) cc_final: 0.6731 (mp) REVERT: B 17 GLN cc_start: 0.7707 (tp-100) cc_final: 0.7289 (tp-100) REVERT: B 175 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: B 197 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7384 (mmm-85) REVERT: B 214 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7522 (mpt-90) REVERT: B 280 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7297 (tmtm) REVERT: G 38 MET cc_start: 0.7107 (ttp) cc_final: 0.6716 (ttm) REVERT: N 32 TYR cc_start: 0.8555 (m-80) cc_final: 0.7958 (m-80) REVERT: N 115 TYR cc_start: 0.8340 (t80) cc_final: 0.8114 (t80) REVERT: N 117 TYR cc_start: 0.8035 (m-10) cc_final: 0.7830 (m-80) outliers start: 31 outliers final: 23 residues processed: 156 average time/residue: 1.0654 time to fit residues: 178.7757 Evaluate side-chains 163 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 170 GLN Chi-restraints excluded: chain P residue 314 VAL Chi-restraints excluded: chain U residue 28 GLU 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 143 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 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 20 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN P 251 ASN ** 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 = 0.4045 r_free = 0.4045 target = 0.168516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135003 restraints weight = 10948.253| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.46 r_work: 0.3522 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8976 Z= 0.239 Angle : 0.542 7.448 12147 Z= 0.281 Chirality : 0.042 0.144 1352 Planarity : 0.003 0.038 1523 Dihedral : 6.580 57.675 1504 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.87 % Allowed : 19.87 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.26), residues: 1051 helix: 2.56 (0.25), residues: 423 sheet: -0.51 (0.33), residues: 215 loop : -1.05 (0.30), residues: 413 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 0.017 0.002 PHE P 256 TYR 0.017 0.001 TYR B 124 ARG 0.007 0.000 ARG P 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6342.00 seconds wall clock time: 112 minutes 43.19 seconds (6763.19 seconds total)