Starting phenix.real_space_refine on Sat Jul 4 02:36:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dp5_27630/07_2026/8dp5_27630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dp5_27630/07_2026/8dp5_27630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dp5_27630/07_2026/8dp5_27630.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dp5_27630/07_2026/8dp5_27630.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dp5_27630/07_2026/8dp5_27630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dp5_27630/07_2026/8dp5_27630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dp5_27630/07_2026/8dp5_27630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dp5_27630/07_2026/8dp5_27630.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.051 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 5623 2.51 5 N 1559 2.21 5 O 1640 1.98 5 H 8916 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17780 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5051 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 34, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5084 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 35, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3691 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain: "D" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3698 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 140 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "P" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 116 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Time building chain proxies: 2.53, per 1000 atoms: 0.14 Number of scatterers: 17780 At special positions: 0 Unit cell: (79.325, 103.54, 154.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 2 15.00 O 1640 8.00 N 1559 7.00 C 5623 6.00 H 8916 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.24 Conformation dependent library (CDL) restraints added in 584.6 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 67.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 130 through 158 Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.016A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.744A pdb=" N ALA A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 299 removed outlier: 3.984A pdb=" N TRP A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 348 through 361 removed outlier: 3.782A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 385 removed outlier: 3.516A pdb=" N ALA A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 400 Processing helix chain 'A' and resid 420 through 442 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.944A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 270 Processing helix chain 'B' and resid 276 through 298 Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 368 through 385 removed outlier: 3.957A pdb=" N ALA B 372 " --> pdb=" O THR B 368 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.506A pdb=" N GLY B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 441 Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.637A pdb=" N GLU B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 Processing helix chain 'C' and resid 4 through 18 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 39 through 71 removed outlier: 3.611A pdb=" N ALA C 56 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 106 removed outlier: 4.335A pdb=" N MET C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 113 through 133 Processing helix chain 'C' and resid 137 through 162 removed outlier: 3.546A pdb=" N GLN C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 183 Processing helix chain 'C' and resid 186 through 203 Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 209 through 232 removed outlier: 4.495A pdb=" N ASP C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 17 Processing helix chain 'D' and resid 19 through 32 removed outlier: 3.655A pdb=" N GLU D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 71 removed outlier: 4.043A pdb=" N ARG D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 107 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 114 through 136 removed outlier: 3.696A pdb=" N LEU D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 163 removed outlier: 4.495A pdb=" N THR D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 184 Processing helix chain 'D' and resid 187 through 204 removed outlier: 3.719A pdb=" N ALA D 204 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 210 through 233 removed outlier: 4.002A pdb=" N ASP D 216 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 220 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 173 removed outlier: 3.704A pdb=" N ALA A 180 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.401A pdb=" N ALA A 252 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 251 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A 236 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 253 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.698A pdb=" N ARG A 260 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA5, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 173 removed outlier: 4.655A pdb=" N ALA B 252 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 235 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 261 removed outlier: 3.660A pdb=" N ARG B 260 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 300 through 302 626 hydrogen bonds defined for protein. 1833 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: 4.01 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.07: 1919 1.07 - 1.26: 8456 1.26 - 1.45: 2272 1.45 - 1.64: 5273 1.64 - 1.83: 59 Bond restraints: 17979 Sorted by residual: bond pdb=" N ILE D 66 " pdb=" H ILE D 66 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CE3 TRP A 279 " pdb=" HE3 TRP A 279 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR D 137 " pdb=" H THR D 137 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLN A 466 " pdb=" H GLN A 466 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ALA C 201 " pdb=" H ALA C 201 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 17974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 28013 2.66 - 5.33: 3541 5.33 - 7.99: 1044 7.99 - 10.65: 20 10.65 - 13.32: 22 Bond angle restraints: 32640 Sorted by residual: angle pdb=" N PRO B 338 " pdb=" CA PRO B 338 " pdb=" C PRO B 338 " ideal model delta sigma weight residual 110.70 119.15 -8.45 1.22e+00 6.72e-01 4.79e+01 angle pdb=" N ALA A 291 " pdb=" CA ALA A 291 " pdb=" C ALA A 291 " ideal model delta sigma weight residual 111.69 103.67 8.02 1.23e+00 6.61e-01 4.26e+01 angle pdb=" C LEU D 163 " pdb=" N PRO D 164 " pdb=" CA PRO D 164 " ideal model delta sigma weight residual 119.66 124.04 -4.38 7.30e-01 1.88e+00 3.60e+01 angle pdb=" CA GLU B 132 " pdb=" C GLU B 132 " pdb=" O GLU B 132 " ideal model delta sigma weight residual 120.90 114.84 6.06 1.03e+00 9.43e-01 3.47e+01 angle pdb=" CA PRO B 338 " pdb=" C PRO B 338 " pdb=" N PRO B 339 " ideal model delta sigma weight residual 117.93 124.70 -6.77 1.20e+00 6.94e-01 3.18e+01 ... (remaining 32635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7795 17.94 - 35.88: 362 35.88 - 53.82: 189 53.82 - 71.75: 93 71.75 - 89.69: 9 Dihedral angle restraints: 8448 sinusoidal: 4687 harmonic: 3761 Sorted by residual: dihedral pdb=" CA GLY B 343 " pdb=" C GLY B 343 " pdb=" N SER B 344 " pdb=" CA SER B 344 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASP B 196 " pdb=" C ASP B 196 " pdb=" N ALA B 197 " pdb=" CA ALA B 197 " ideal model delta harmonic sigma weight residual 180.00 154.85 25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ASP A 196 " pdb=" C ASP A 196 " pdb=" N ALA A 197 " pdb=" CA ALA A 197 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 8445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 970 0.089 - 0.178: 345 0.178 - 0.267: 60 0.267 - 0.357: 7 0.357 - 0.446: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA LYS D 73 " pdb=" N LYS D 73 " pdb=" C LYS D 73 " pdb=" CB LYS D 73 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA LEU B 253 " pdb=" N LEU B 253 " pdb=" C LEU B 253 " pdb=" CB LEU B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA ASN D 186 " pdb=" N ASN D 186 " pdb=" C ASN D 186 " pdb=" CB ASN D 186 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1381 not shown) Planarity restraints: 2655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 472 " 0.216 2.00e-02 2.50e+03 7.21e-02 2.08e+02 pdb=" CG TRP A 472 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP A 472 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP A 472 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP A 472 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP A 472 " -0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP A 472 " -0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 472 " 0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 472 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 472 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP A 472 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP A 472 " -0.043 2.00e-02 2.50e+03 pdb=" HE3 TRP A 472 " -0.093 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 472 " 0.057 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 472 " -0.009 2.00e-02 2.50e+03 pdb=" HH2 TRP A 472 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 423 " 0.165 2.00e-02 2.50e+03 6.57e-02 1.73e+02 pdb=" CG TRP B 423 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP B 423 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 423 " -0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP B 423 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TRP B 423 " -0.037 2.00e-02 2.50e+03 pdb=" CE3 TRP B 423 " -0.066 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 423 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 423 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP B 423 " 0.041 2.00e-02 2.50e+03 pdb=" HD1 TRP B 423 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 TRP B 423 " -0.067 2.00e-02 2.50e+03 pdb=" HE3 TRP B 423 " -0.093 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 423 " 0.037 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 423 " -0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP B 423 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 60 " -0.152 2.00e-02 2.50e+03 6.14e-02 1.51e+02 pdb=" CG TRP D 60 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP D 60 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 60 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP D 60 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TRP D 60 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 60 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 60 " -0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 60 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP D 60 " -0.040 2.00e-02 2.50e+03 pdb=" HD1 TRP D 60 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TRP D 60 " 0.106 2.00e-02 2.50e+03 pdb=" HE3 TRP D 60 " 0.089 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 60 " -0.056 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 60 " 0.033 2.00e-02 2.50e+03 pdb=" HH2 TRP D 60 " -0.069 2.00e-02 2.50e+03 ... (remaining 2652 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 263 1.95 - 2.61: 17111 2.61 - 3.28: 53833 3.28 - 3.94: 67856 3.94 - 4.60: 100067 Nonbonded interactions: 239130 Sorted by model distance: nonbonded pdb="HD11 LEU C 205 " pdb=" HD1 TYR C 213 " model vdw 1.288 2.270 nonbonded pdb=" OE2 GLU D 183 " pdb=" HG1 THR P 67 " model vdw 1.548 2.450 nonbonded pdb="HD21 LEU A 356 " pdb=" HB1 ALA A 378 " model vdw 1.582 2.440 nonbonded pdb=" HG SER D 210 " pdb=" OE2 GLU D 212 " model vdw 1.595 2.450 nonbonded pdb=" OE2 GLU D 36 " pdb=" HG SER D 117 " model vdw 1.601 2.450 ... (remaining 239125 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 130 through 472) selection = (chain 'B' and (resid 130 through 406 or resid 419 through 472)) } ncs_group { reference = (chain 'E' and resid 66 through 72) selection = chain 'P' } 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: 3.350 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: 0.120 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.520 Find NCS groups from input model: 0.150 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 0.013 0.140 9063 Z= 0.817 Angle : 1.783 12.815 12331 Z= 1.232 Chirality : 0.089 0.446 1384 Planarity : 0.016 0.192 1598 Dihedral : 12.279 89.692 3379 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.22), residues: 1123 helix: -0.23 (0.16), residues: 707 sheet: 0.71 (0.60), residues: 82 loop : -0.48 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 333 TYR 0.134 0.015 TYR C 127 PHE 0.041 0.009 PHE C 176 TRP 0.149 0.019 TRP A 472 HIS 0.010 0.002 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.01291 / 0.82 ( 9063) covalent geometry : angle 1.78283 / 1.23 (12331) hydrogen bonds : bond 0.21471 / 15.28 ( 618) hydrogen bonds : angle 6.71348 / 4.79 ( 1833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ASP cc_start: 0.6794 (t0) cc_final: 0.6389 (t0) REVERT: B 207 LYS cc_start: 0.7442 (tttt) cc_final: 0.7215 (tttp) REVERT: C 193 LEU cc_start: 0.7334 (tp) cc_final: 0.7030 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2363 time to fit residues: 41.1918 Evaluate side-chains 66 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS B 135 HIS C 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.139154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099930 restraints weight = 37231.694| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.85 r_work: 0.3204 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9063 Z= 0.176 Angle : 0.657 7.350 12331 Z= 0.353 Chirality : 0.038 0.145 1384 Planarity : 0.006 0.063 1598 Dihedral : 5.326 31.874 1250 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.43 % Allowed : 3.14 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.24), residues: 1123 helix: 1.80 (0.18), residues: 714 sheet: -0.54 (0.53), residues: 97 loop : -0.32 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 427 TYR 0.019 0.002 TYR C 127 PHE 0.015 0.002 PHE D 177 TRP 0.017 0.001 TRP A 472 HIS 0.009 0.002 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 9063) covalent geometry : angle 0.65706 / 0.35 (12331) hydrogen bonds : bond 0.08118 / 5.80 ( 618) hydrogen bonds : angle 4.68144 / 3.39 ( 1833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 175 ASP cc_start: 0.7109 (t0) cc_final: 0.6849 (t0) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.2623 time to fit residues: 25.3461 Evaluate side-chains 62 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 189 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.138855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099472 restraints weight = 37427.889| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.89 r_work: 0.3195 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9063 Z= 0.152 Angle : 0.564 6.601 12331 Z= 0.293 Chirality : 0.036 0.136 1384 Planarity : 0.005 0.052 1598 Dihedral : 4.813 36.586 1250 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.22 % Allowed : 4.11 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.25), residues: 1123 helix: 2.42 (0.19), residues: 716 sheet: -0.94 (0.51), residues: 99 loop : -0.53 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 169 TYR 0.018 0.002 TYR C 127 PHE 0.012 0.001 PHE D 120 TRP 0.011 0.001 TRP A 472 HIS 0.008 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9063) covalent geometry : angle 0.56356 / 0.29 (12331) hydrogen bonds : bond 0.06521 / 4.67 ( 618) hydrogen bonds : angle 4.15543 / 3.02 ( 1833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.455 Fit side-chains REVERT: A 219 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6884 (mp0) REVERT: B 175 ASP cc_start: 0.7252 (t0) cc_final: 0.7035 (t70) REVERT: C 181 TYR cc_start: 0.8018 (t80) cc_final: 0.7674 (t80) outliers start: 2 outliers final: 0 residues processed: 68 average time/residue: 0.2788 time to fit residues: 24.7965 Evaluate side-chains 56 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 13 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.138645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099161 restraints weight = 37346.244| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.90 r_work: 0.3249 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9063 Z= 0.145 Angle : 0.527 7.250 12331 Z= 0.272 Chirality : 0.035 0.138 1384 Planarity : 0.005 0.052 1598 Dihedral : 4.566 37.619 1250 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.22 % Allowed : 4.86 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.25), residues: 1123 helix: 2.81 (0.19), residues: 715 sheet: -0.86 (0.52), residues: 93 loop : -0.52 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 438 TYR 0.015 0.001 TYR C 127 PHE 0.011 0.001 PHE D 120 TRP 0.010 0.001 TRP A 472 HIS 0.005 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 9063) covalent geometry : angle 0.52691 / 0.27 (12331) hydrogen bonds : bond 0.05726 / 4.09 ( 618) hydrogen bonds : angle 3.89102 / 2.83 ( 1833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.508 Fit side-chains REVERT: A 196 ASP cc_start: 0.7686 (t0) cc_final: 0.7415 (t0) REVERT: C 83 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7489 (tm-30) REVERT: C 162 MET cc_start: 0.7664 (mtp) cc_final: 0.7388 (mtp) REVERT: C 215 ASP cc_start: 0.7761 (m-30) cc_final: 0.7109 (t70) outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.3068 time to fit residues: 25.6389 Evaluate side-chains 57 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101605 restraints weight = 37075.805| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.83 r_work: 0.3286 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9063 Z= 0.103 Angle : 0.483 6.300 12331 Z= 0.246 Chirality : 0.034 0.134 1384 Planarity : 0.005 0.051 1598 Dihedral : 4.351 35.197 1250 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.11 % Allowed : 5.41 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.25), residues: 1123 helix: 3.11 (0.19), residues: 718 sheet: -0.87 (0.51), residues: 93 loop : -0.27 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 438 TYR 0.012 0.001 TYR C 127 PHE 0.007 0.001 PHE D 120 TRP 0.008 0.001 TRP B 198 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 9063) covalent geometry : angle 0.48334 / 0.25 (12331) hydrogen bonds : bond 0.04916 / 3.51 ( 618) hydrogen bonds : angle 3.68210 / 2.66 ( 1833) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.483 Fit side-chains REVERT: A 196 ASP cc_start: 0.7674 (t0) cc_final: 0.7387 (t0) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.2753 time to fit residues: 22.7777 Evaluate side-chains 57 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.139814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100846 restraints weight = 36813.862| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.81 r_work: 0.3273 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9063 Z= 0.119 Angle : 0.482 6.021 12331 Z= 0.243 Chirality : 0.034 0.133 1384 Planarity : 0.004 0.048 1598 Dihedral : 4.232 35.490 1250 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.32 % Allowed : 5.95 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.25), residues: 1123 helix: 3.24 (0.19), residues: 718 sheet: -0.94 (0.50), residues: 93 loop : -0.21 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 154 TYR 0.014 0.001 TYR C 127 PHE 0.009 0.001 PHE D 120 TRP 0.009 0.001 TRP A 472 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9063) covalent geometry : angle 0.48158 / 0.24 (12331) hydrogen bonds : bond 0.04815 / 3.44 ( 618) hydrogen bonds : angle 3.60232 / 2.61 ( 1833) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7688 (t0) cc_final: 0.7399 (t0) REVERT: B 256 GLU cc_start: 0.8103 (mp0) cc_final: 0.7876 (mp0) REVERT: C 83 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7457 (tm-30) outliers start: 3 outliers final: 1 residues processed: 66 average time/residue: 0.2724 time to fit residues: 23.5532 Evaluate side-chains 62 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.137841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098765 restraints weight = 37235.721| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.81 r_work: 0.3185 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9063 Z= 0.152 Angle : 0.505 7.156 12331 Z= 0.256 Chirality : 0.035 0.134 1384 Planarity : 0.005 0.045 1598 Dihedral : 4.259 37.783 1250 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.22 % Allowed : 6.38 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.25), residues: 1123 helix: 3.13 (0.18), residues: 720 sheet: -0.96 (0.50), residues: 93 loop : -0.40 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.014 0.001 TYR C 127 PHE 0.012 0.001 PHE D 120 TRP 0.011 0.001 TRP A 472 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 9063) covalent geometry : angle 0.50496 / 0.26 (12331) hydrogen bonds : bond 0.05260 / 3.76 ( 618) hydrogen bonds : angle 3.65895 / 2.64 ( 1833) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7775 (t0) cc_final: 0.7505 (t0) REVERT: B 256 GLU cc_start: 0.8133 (mp0) cc_final: 0.7890 (mp0) REVERT: C 83 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7387 (tm-30) outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.2606 time to fit residues: 21.5252 Evaluate side-chains 62 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.0270 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.139299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100358 restraints weight = 37040.342| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.81 r_work: 0.3264 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9063 Z= 0.110 Angle : 0.471 5.774 12331 Z= 0.238 Chirality : 0.034 0.129 1384 Planarity : 0.004 0.044 1598 Dihedral : 4.141 38.358 1250 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.11 % Allowed : 6.92 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.25), residues: 1123 helix: 3.28 (0.18), residues: 720 sheet: -0.95 (0.50), residues: 93 loop : -0.28 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.014 0.001 TYR D 214 PHE 0.008 0.001 PHE B 171 TRP 0.011 0.001 TRP A 472 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9063) covalent geometry : angle 0.47118 / 0.24 (12331) hydrogen bonds : bond 0.04715 / 3.37 ( 618) hydrogen bonds : angle 3.52933 / 2.54 ( 1833) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7712 (t0) cc_final: 0.7443 (t0) REVERT: B 256 GLU cc_start: 0.8096 (mp0) cc_final: 0.7849 (mp0) outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.3038 time to fit residues: 26.5059 Evaluate side-chains 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.138789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099913 restraints weight = 37112.464| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.81 r_work: 0.3205 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9063 Z= 0.129 Angle : 0.478 5.680 12331 Z= 0.241 Chirality : 0.034 0.134 1384 Planarity : 0.005 0.043 1598 Dihedral : 4.126 39.217 1250 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.11 % Allowed : 7.03 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.25), residues: 1123 helix: 3.28 (0.18), residues: 720 sheet: -1.01 (0.50), residues: 93 loop : -0.31 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.014 0.001 TYR C 127 PHE 0.010 0.001 PHE D 120 TRP 0.011 0.001 TRP A 472 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9063) covalent geometry : angle 0.47773 / 0.24 (12331) hydrogen bonds : bond 0.04805 / 3.44 ( 618) hydrogen bonds : angle 3.53634 / 2.55 ( 1833) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7761 (t0) cc_final: 0.7501 (t0) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.2981 time to fit residues: 25.0958 Evaluate side-chains 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 73 optimal weight: 0.0370 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.139612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100547 restraints weight = 37056.746| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.87 r_work: 0.3270 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9063 Z= 0.104 Angle : 0.462 5.712 12331 Z= 0.232 Chirality : 0.033 0.130 1384 Planarity : 0.004 0.042 1598 Dihedral : 4.063 41.949 1250 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.11 % Allowed : 7.03 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.25), residues: 1123 helix: 3.37 (0.18), residues: 720 sheet: -0.97 (0.49), residues: 93 loop : -0.24 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.012 0.001 TYR C 127 PHE 0.008 0.001 PHE D 120 TRP 0.012 0.001 TRP A 472 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 9063) covalent geometry : angle 0.46205 / 0.23 (12331) hydrogen bonds : bond 0.04498 / 3.21 ( 618) hydrogen bonds : angle 3.46116 / 2.49 ( 1833) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7721 (t0) cc_final: 0.7457 (t0) REVERT: C 181 TYR cc_start: 0.8211 (t80) cc_final: 0.7844 (t80) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.2658 time to fit residues: 21.8179 Evaluate side-chains 63 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.139438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100642 restraints weight = 37051.615| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.81 r_work: 0.3273 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9063 Z= 0.114 Angle : 0.465 5.645 12331 Z= 0.233 Chirality : 0.033 0.132 1384 Planarity : 0.004 0.042 1598 Dihedral : 4.028 43.930 1250 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.11 % Allowed : 7.14 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.25), residues: 1123 helix: 3.38 (0.18), residues: 721 sheet: -1.00 (0.49), residues: 93 loop : -0.26 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.014 0.001 TYR C 127 PHE 0.009 0.001 PHE D 120 TRP 0.013 0.001 TRP A 472 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 9063) covalent geometry : angle 0.46500 / 0.23 (12331) hydrogen bonds : bond 0.04509 / 3.22 ( 618) hydrogen bonds : angle 3.45750 / 2.48 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3570.39 seconds wall clock time: 61 minutes 13.89 seconds (3673.89 seconds total)