Starting phenix.real_space_refine on Sun Aug 24 06:49:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dp5_27630/08_2025/8dp5_27630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dp5_27630/08_2025/8dp5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dp5_27630/08_2025/8dp5_27630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dp5_27630/08_2025/8dp5_27630.map" model { file = "/net/cci-nas-00/data/ceres_data/8dp5_27630/08_2025/8dp5_27630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dp5_27630/08_2025/8dp5_27630.cif" } 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-2.0-5787/lib/python3.9/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: 3.70, per 1000 atoms: 0.21 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: 1.48 Conformation dependent library (CDL) restraints added in 622.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.51 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: 4.08 Time building geometry restraints manager: 2.20 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: 7797 17.94 - 35.88: 362 35.88 - 53.82: 189 53.82 - 71.75: 93 71.75 - 89.69: 9 Dihedral angle restraints: 8450 sinusoidal: 4689 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 8447 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: 2.390 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: 0.130 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.480 Find NCS groups from input model: 0.170 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 aren 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 covalent geometry : bond 0.01291 ( 9063) covalent geometry : angle 1.78283 (12331) hydrogen bonds : bond 0.21471 ( 618) hydrogen bonds : angle 6.71348 ( 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 : 0.563 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: 0.3049 time to fit residues: 51.9592 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 : 0.469 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3932 r_free = 0.3932 target = 0.139042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099743 restraints weight = 37182.012| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.88 r_work: 0.3199 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9063 Z= 0.177 Angle : 0.657 7.337 12331 Z= 0.353 Chirality : 0.038 0.146 1384 Planarity : 0.007 0.063 1598 Dihedral : 5.328 31.875 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 aren not related in a simple way. whole: 1.49 (0.24), residues: 1123 helix: 1.80 (0.18), residues: 714 sheet: -0.53 (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 covalent geometry : bond 0.00384 ( 9063) covalent geometry : angle 0.65724 (12331) hydrogen bonds : bond 0.08148 ( 618) hydrogen bonds : angle 4.68146 ( 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 : 0.607 Fit side-chains revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 175 ASP cc_start: 0.7117 (t0) cc_final: 0.6898 (t0) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.3245 time to fit residues: 30.6279 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 : 0.490 ------------------------------------------------------------------------------- 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: 0.2980 chunk 97 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101809 restraints weight = 37249.446| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.84 r_work: 0.3290 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9063 Z= 0.128 Angle : 0.545 6.687 12331 Z= 0.281 Chirality : 0.035 0.136 1384 Planarity : 0.005 0.051 1598 Dihedral : 4.686 35.399 1250 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.11 % Allowed : 3.89 % Favored : 96.00 % 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 aren not related in a simple way. whole: 2.23 (0.25), residues: 1123 helix: 2.60 (0.19), residues: 715 sheet: -0.75 (0.53), residues: 93 loop : -0.47 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 169 TYR 0.016 0.001 TYR C 127 PHE 0.010 0.001 PHE D 120 TRP 0.009 0.001 TRP A 472 HIS 0.007 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9063) covalent geometry : angle 0.54524 (12331) hydrogen bonds : bond 0.05918 ( 618) hydrogen bonds : angle 4.01645 ( 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 69 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.521 Fit side-chains REVERT: A 219 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7068 (mp0) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.3227 time to fit residues: 28.8672 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 : 0.507 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 56 optimal weight: 6.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.140394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101305 restraints weight = 37189.478| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.84 r_work: 0.3282 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3369 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= 0.122 Angle : 0.507 6.230 12331 Z= 0.260 Chirality : 0.034 0.136 1384 Planarity : 0.005 0.050 1598 Dihedral : 4.462 35.152 1250 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.22 % Allowed : 4.65 % Favored : 95.14 % 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 aren not related in a simple way. whole: 2.69 (0.25), residues: 1123 helix: 3.00 (0.19), residues: 718 sheet: -0.88 (0.51), residues: 93 loop : -0.32 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.013 0.001 TYR C 127 PHE 0.009 0.001 PHE D 120 TRP 0.009 0.001 TRP A 472 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9063) covalent geometry : angle 0.50687 (12331) hydrogen bonds : bond 0.05293 ( 618) hydrogen bonds : angle 3.78414 ( 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 : 0.662 Fit side-chains revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7637 (t0) cc_final: 0.7372 (t0) REVERT: C 83 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7449 (tm-30) outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.3551 time to fit residues: 28.5555 Evaluate side-chains 58 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 94 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.141012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102133 restraints weight = 37130.146| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.83 r_work: 0.3292 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9063 Z= 0.107 Angle : 0.482 5.791 12331 Z= 0.244 Chirality : 0.034 0.131 1384 Planarity : 0.005 0.053 1598 Dihedral : 4.272 34.147 1250 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.22 % Allowed : 5.19 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.25), residues: 1123 helix: 3.18 (0.18), residues: 718 sheet: -0.89 (0.51), residues: 93 loop : -0.20 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 225 TYR 0.012 0.001 TYR C 127 PHE 0.008 0.001 PHE D 120 TRP 0.008 0.001 TRP A 472 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9063) covalent geometry : angle 0.48219 (12331) hydrogen bonds : bond 0.04846 ( 618) hydrogen bonds : angle 3.64264 ( 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 65 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7638 (t0) cc_final: 0.7346 (t0) outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 0.3336 time to fit residues: 27.8287 Evaluate side-chains 60 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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: 1.9990 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.138756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099925 restraints weight = 36897.125| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.80 r_work: 0.3260 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9063 Z= 0.151 Angle : 0.496 5.800 12331 Z= 0.253 Chirality : 0.035 0.136 1384 Planarity : 0.005 0.045 1598 Dihedral : 4.258 36.084 1250 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.32 % Allowed : 6.27 % 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 aren not related in a simple way. whole: 2.88 (0.25), residues: 1123 helix: 3.18 (0.19), residues: 718 sheet: -0.93 (0.50), residues: 93 loop : -0.29 (0.34), residues: 312 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 0.011 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 covalent geometry : bond 0.00362 ( 9063) covalent geometry : angle 0.49644 (12331) hydrogen bonds : bond 0.05149 ( 618) hydrogen bonds : angle 3.65082 ( 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 63 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7672 (t0) cc_final: 0.7378 (t0) REVERT: C 83 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7463 (tm-30) outliers start: 3 outliers final: 1 residues processed: 63 average time/residue: 0.3421 time to fit residues: 27.7307 Evaluate side-chains 59 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 0.0670 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.139971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100760 restraints weight = 37105.778| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.88 r_work: 0.3269 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3818 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= 0.109 Angle : 0.473 5.757 12331 Z= 0.239 Chirality : 0.034 0.133 1384 Planarity : 0.004 0.044 1598 Dihedral : 4.154 36.283 1250 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.22 % Allowed : 6.49 % Favored : 93.30 % 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 aren not related in a simple way. whole: 3.04 (0.25), residues: 1123 helix: 3.28 (0.19), residues: 720 sheet: -0.90 (0.50), residues: 93 loop : -0.19 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.012 0.001 TYR C 127 PHE 0.009 0.001 PHE B 171 TRP 0.010 0.001 TRP A 472 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9063) covalent geometry : angle 0.47259 (12331) hydrogen bonds : bond 0.04728 ( 618) hydrogen bonds : angle 3.54213 ( 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 65 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7697 (t0) cc_final: 0.7404 (t0) outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.3490 time to fit residues: 28.8618 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 : 0.497 ------------------------------------------------------------------------------- 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: 0.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.140706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101606 restraints weight = 36974.291| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.88 r_work: 0.3287 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4005 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 : 0.461 5.700 12331 Z= 0.231 Chirality : 0.034 0.133 1384 Planarity : 0.004 0.045 1598 Dihedral : 4.015 39.670 1250 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.11 % Allowed : 6.81 % Favored : 93.08 % 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 aren not related in a simple way. whole: 3.17 (0.25), residues: 1123 helix: 3.42 (0.19), residues: 720 sheet: -0.99 (0.49), residues: 93 loop : -0.18 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 383 TYR 0.023 0.001 TYR B 188 PHE 0.009 0.001 PHE B 171 TRP 0.011 0.001 TRP A 472 HIS 0.006 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9063) covalent geometry : angle 0.46119 (12331) hydrogen bonds : bond 0.04361 ( 618) hydrogen bonds : angle 3.44717 ( 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 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7668 (t0) cc_final: 0.7371 (t0) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.3373 time to fit residues: 27.7734 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 : 0.506 ------------------------------------------------------------------------------- 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: 9.9990 chunk 76 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.138870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099702 restraints weight = 37116.441| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.87 r_work: 0.3264 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4021 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= 0.139 Angle : 0.478 5.676 12331 Z= 0.241 Chirality : 0.034 0.135 1384 Planarity : 0.005 0.043 1598 Dihedral : 4.070 40.410 1250 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.32 % Allowed : 7.03 % Favored : 92.65 % 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 aren not related in a simple way. whole: 3.04 (0.25), residues: 1123 helix: 3.33 (0.18), residues: 720 sheet: -0.98 (0.49), residues: 93 loop : -0.31 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 172 TYR 0.013 0.001 TYR C 127 PHE 0.011 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 covalent geometry : bond 0.00334 ( 9063) covalent geometry : angle 0.47821 (12331) hydrogen bonds : bond 0.04831 ( 618) hydrogen bonds : angle 3.51319 ( 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 66 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7684 (t0) cc_final: 0.7409 (t0) REVERT: B 256 GLU cc_start: 0.8178 (mp0) cc_final: 0.7957 (mp0) outliers start: 3 outliers final: 1 residues processed: 66 average time/residue: 0.3253 time to fit residues: 27.7829 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 : 0.489 ------------------------------------------------------------------------------- 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: 0.3980 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 0.0070 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.140604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.101684 restraints weight = 37013.481| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.88 r_work: 0.3234 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4142 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= 0.091 Angle : 0.452 5.612 12331 Z= 0.227 Chirality : 0.033 0.134 1384 Planarity : 0.004 0.040 1598 Dihedral : 3.979 43.989 1250 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.11 % Allowed : 7.35 % Favored : 92.54 % 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 aren not related in a simple way. whole: 3.25 (0.25), residues: 1123 helix: 3.48 (0.19), residues: 720 sheet: -0.96 (0.49), residues: 93 loop : -0.15 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 383 TYR 0.013 0.001 TYR B 188 PHE 0.007 0.001 PHE B 171 TRP 0.011 0.001 TRP A 472 HIS 0.003 0.000 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 9063) covalent geometry : angle 0.45159 (12331) hydrogen bonds : bond 0.04256 ( 618) hydrogen bonds : angle 3.39993 ( 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 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7705 (t0) cc_final: 0.7416 (t0) REVERT: B 256 GLU cc_start: 0.8120 (mp0) cc_final: 0.7889 (mp0) REVERT: C 181 TYR cc_start: 0.8110 (t80) cc_final: 0.7706 (t80) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.3306 time to fit residues: 27.2322 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 : 0.498 ------------------------------------------------------------------------------- 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: 4.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 46 optimal weight: 0.0270 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.139026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100360 restraints weight = 37115.034| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.80 r_work: 0.3272 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4144 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= 0.133 Angle : 0.468 5.562 12331 Z= 0.235 Chirality : 0.034 0.135 1384 Planarity : 0.004 0.041 1598 Dihedral : 4.007 44.343 1250 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.11 % Allowed : 7.57 % Favored : 92.32 % 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 aren not related in a simple way. whole: 3.15 (0.25), residues: 1123 helix: 3.41 (0.18), residues: 721 sheet: -1.00 (0.49), residues: 93 loop : -0.23 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 438 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 0.004 0.001 HIS B 135 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9063) covalent geometry : angle 0.46802 (12331) hydrogen bonds : bond 0.04657 ( 618) hydrogen bonds : angle 3.45828 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3937.31 seconds wall clock time: 67 minutes 46.81 seconds (4066.81 seconds total)