Starting phenix.real_space_refine on Sun Jun 15 21:15:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dp5_27630/06_2025/8dp5_27630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dp5_27630/06_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_27630/06_2025/8dp5_27630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dp5_27630/06_2025/8dp5_27630.map" model { file = "/net/cci-nas-00/data/ceres_data/8dp5_27630/06_2025/8dp5_27630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dp5_27630/06_2025/8dp5_27630.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.051 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.24, per 1000 atoms: 0.58 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: 4.21 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.38 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: 8.75 Time building geometry restraints manager: 5.23 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: 198.570 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: 0.340 Extract box with map and model: 6.850 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 45.520 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (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 TRP 0.149 0.019 TRP A 472 HIS 0.010 0.002 HIS A 166 PHE 0.041 0.009 PHE C 176 TYR 0.134 0.015 TYR C 127 ARG 0.013 0.001 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.21471 ( 618) hydrogen bonds : angle 6.71348 ( 1833) covalent geometry : bond 0.01291 ( 9063) covalent geometry : angle 1.78283 (12331) *********************** 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 : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ASP cc_start: 0.6794 (t0) cc_final: 0.6534 (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: 0.7036 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.6790 time to fit residues: 117.8619 Evaluate side-chains 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS C 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.139567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098721 restraints weight = 37715.927| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.98 r_work: 0.3196 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9063 Z= 0.182 Angle : 0.653 7.356 12331 Z= 0.352 Chirality : 0.038 0.143 1384 Planarity : 0.006 0.062 1598 Dihedral : 5.294 31.751 1250 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1123 helix: 1.81 (0.18), residues: 714 sheet: -0.50 (0.53), residues: 97 loop : -0.31 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 472 HIS 0.011 0.002 HIS C 166 PHE 0.015 0.002 PHE D 177 TYR 0.020 0.002 TYR C 127 ARG 0.005 0.001 ARG B 427 Details of bonding type rmsd hydrogen bonds : bond 0.08015 ( 618) hydrogen bonds : angle 4.65881 ( 1833) covalent geometry : bond 0.00374 ( 9063) covalent geometry : angle 0.65342 (12331) *********************** 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 : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7664 (mt-10) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.7256 time to fit residues: 71.4569 Evaluate side-chains 61 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098491 restraints weight = 37095.010| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.86 r_work: 0.3178 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9063 Z= 0.177 Angle : 0.582 6.576 12331 Z= 0.303 Chirality : 0.037 0.138 1384 Planarity : 0.005 0.051 1598 Dihedral : 4.859 38.597 1250 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.32 % Allowed : 4.11 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1123 helix: 2.36 (0.19), residues: 716 sheet: -0.92 (0.51), residues: 99 loop : -0.60 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.007 0.001 HIS B 166 PHE 0.013 0.001 PHE D 120 TYR 0.019 0.002 TYR C 127 ARG 0.003 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.06694 ( 618) hydrogen bonds : angle 4.18475 ( 1833) covalent geometry : bond 0.00412 ( 9063) covalent geometry : angle 0.58192 (12331) *********************** 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 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 1.931 Fit side-chains revert: symmetry clash REVERT: A 219 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6884 (mp0) REVERT: B 171 PHE cc_start: 0.8125 (m-80) cc_final: 0.7918 (m-80) outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 0.7886 time to fit residues: 66.6883 Evaluate side-chains 53 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.136952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097529 restraints weight = 37496.972| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.88 r_work: 0.3165 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9063 Z= 0.179 Angle : 0.549 7.666 12331 Z= 0.285 Chirality : 0.036 0.134 1384 Planarity : 0.005 0.050 1598 Dihedral : 4.688 39.747 1250 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.22 % Allowed : 4.76 % Favored : 95.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.25), residues: 1123 helix: 2.60 (0.19), residues: 716 sheet: -0.87 (0.51), residues: 99 loop : -0.59 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.011 0.001 HIS B 166 PHE 0.012 0.001 PHE D 120 TYR 0.016 0.002 TYR C 127 ARG 0.003 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.06194 ( 618) hydrogen bonds : angle 4.03051 ( 1833) covalent geometry : bond 0.00430 ( 9063) covalent geometry : angle 0.54902 (12331) *********************** 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 61 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7396 (tm-30) REVERT: C 215 ASP cc_start: 0.7741 (m-30) cc_final: 0.7027 (t70) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.7412 time to fit residues: 59.4489 Evaluate side-chains 56 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.138247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099113 restraints weight = 37433.976| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.83 r_work: 0.3249 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3465 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= 0.134 Angle : 0.510 6.851 12331 Z= 0.262 Chirality : 0.035 0.133 1384 Planarity : 0.005 0.048 1598 Dihedral : 4.474 38.954 1250 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.22 % Allowed : 5.08 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.25), residues: 1123 helix: 2.89 (0.18), residues: 718 sheet: -0.78 (0.52), residues: 93 loop : -0.47 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 198 HIS 0.009 0.001 HIS B 166 PHE 0.010 0.001 PHE D 120 TYR 0.015 0.001 TYR C 127 ARG 0.001 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.05485 ( 618) hydrogen bonds : angle 3.81619 ( 1833) covalent geometry : bond 0.00311 ( 9063) covalent geometry : angle 0.51005 (12331) *********************** 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 61 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7627 (t0) cc_final: 0.7406 (t0) REVERT: C 83 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7422 (tm-30) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.7342 time to fit residues: 58.8585 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 : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.138798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099740 restraints weight = 37090.315| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.81 r_work: 0.3201 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3637 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= 0.122 Angle : 0.493 6.410 12331 Z= 0.251 Chirality : 0.034 0.131 1384 Planarity : 0.005 0.047 1598 Dihedral : 4.319 38.033 1250 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.22 % Allowed : 5.95 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.25), residues: 1123 helix: 3.11 (0.18), residues: 717 sheet: -0.81 (0.52), residues: 93 loop : -0.38 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.012 0.001 HIS B 166 PHE 0.014 0.001 PHE B 171 TYR 0.014 0.001 TYR C 127 ARG 0.003 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 618) hydrogen bonds : angle 3.69341 ( 1833) covalent geometry : bond 0.00281 ( 9063) covalent geometry : angle 0.49304 (12331) *********************** 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 69 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7717 (t0) cc_final: 0.7461 (t0) REVERT: B 256 GLU cc_start: 0.8094 (mp0) cc_final: 0.7880 (mp0) REVERT: C 83 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7306 (tm-30) REVERT: C 181 TYR cc_start: 0.8196 (t80) cc_final: 0.7938 (t80) outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.6514 time to fit residues: 59.2717 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 : 1.267 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.139040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100028 restraints weight = 37046.821| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.82 r_work: 0.3205 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3807 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= 0.115 Angle : 0.478 5.852 12331 Z= 0.243 Chirality : 0.034 0.131 1384 Planarity : 0.005 0.046 1598 Dihedral : 4.229 37.193 1250 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.11 % Allowed : 6.27 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.25), residues: 1123 helix: 3.20 (0.18), residues: 718 sheet: -0.79 (0.52), residues: 93 loop : -0.31 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.010 0.001 HIS B 166 PHE 0.008 0.001 PHE D 120 TYR 0.017 0.001 TYR C 181 ARG 0.004 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 618) hydrogen bonds : angle 3.60110 ( 1833) covalent geometry : bond 0.00262 ( 9063) covalent geometry : angle 0.47826 (12331) *********************** 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: 1 poor density : 62 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7703 (t0) cc_final: 0.7433 (t0) REVERT: B 256 GLU cc_start: 0.8134 (mp0) cc_final: 0.7903 (mp0) REVERT: C 83 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7298 (tm-30) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.6432 time to fit residues: 53.3320 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 : 1.267 ------------------------------------------------------------------------------- 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 83 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.137602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098500 restraints weight = 37192.195| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.81 r_work: 0.3185 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9063 Z= 0.152 Angle : 0.499 5.987 12331 Z= 0.253 Chirality : 0.035 0.134 1384 Planarity : 0.005 0.044 1598 Dihedral : 4.249 39.294 1250 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.25), residues: 1123 helix: 3.11 (0.18), residues: 720 sheet: -0.87 (0.51), residues: 99 loop : -0.36 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.010 0.001 HIS B 166 PHE 0.011 0.001 PHE D 120 TYR 0.015 0.001 TYR C 127 ARG 0.002 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 618) hydrogen bonds : angle 3.64468 ( 1833) covalent geometry : bond 0.00363 ( 9063) covalent geometry : angle 0.49924 (12331) *********************** 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 : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7730 (t0) cc_final: 0.7462 (t0) REVERT: B 256 GLU cc_start: 0.8121 (mp0) cc_final: 0.7880 (mp0) REVERT: C 83 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7295 (tm-30) outliers start: 1 outliers final: 1 residues processed: 64 average time/residue: 0.6782 time to fit residues: 56.1030 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 : 1.378 ------------------------------------------------------------------------------- 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 3 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 0.0040 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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 = 0.138955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100047 restraints weight = 37028.029| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.80 r_work: 0.3270 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3981 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 : 0.473 5.722 12331 Z= 0.240 Chirality : 0.034 0.130 1384 Planarity : 0.005 0.045 1598 Dihedral : 4.163 38.219 1250 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.25), residues: 1123 helix: 3.24 (0.18), residues: 720 sheet: -0.80 (0.51), residues: 93 loop : -0.31 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.008 0.001 HIS B 166 PHE 0.008 0.001 PHE D 120 TYR 0.013 0.001 TYR C 127 ARG 0.004 0.000 ARG B 383 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 618) hydrogen bonds : angle 3.55089 ( 1833) covalent geometry : bond 0.00262 ( 9063) covalent geometry : angle 0.47291 (12331) *********************** 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 65 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7633 (t0) cc_final: 0.7359 (t0) REVERT: B 256 GLU cc_start: 0.8135 (mp0) cc_final: 0.7909 (mp0) REVERT: C 83 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7377 (tm-30) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.6412 time to fit residues: 55.1749 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 : 1.412 ------------------------------------------------------------------------------- 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 105 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.140484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101377 restraints weight = 37045.079| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.88 r_work: 0.3288 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9063 Z= 0.096 Angle : 0.461 6.269 12331 Z= 0.231 Chirality : 0.033 0.129 1384 Planarity : 0.004 0.045 1598 Dihedral : 4.025 42.063 1250 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.26), residues: 1123 helix: 3.43 (0.19), residues: 720 sheet: -0.84 (0.50), residues: 93 loop : -0.21 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.009 0.001 HIS B 166 PHE 0.008 0.001 PHE B 171 TYR 0.017 0.001 TYR B 188 ARG 0.004 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 618) hydrogen bonds : angle 3.43049 ( 1833) covalent geometry : bond 0.00211 ( 9063) covalent geometry : angle 0.46121 (12331) ********************** 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 62 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7634 (t0) cc_final: 0.7359 (t0) REVERT: C 83 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7339 (tm-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.6680 time to fit residues: 54.2222 Evaluate side-chains 59 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.140060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101054 restraints weight = 37070.108| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.83 r_work: 0.3225 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4152 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= 0.107 Angle : 0.460 5.655 12331 Z= 0.230 Chirality : 0.033 0.130 1384 Planarity : 0.004 0.045 1598 Dihedral : 4.006 43.641 1250 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.22 % Allowed : 7.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.26), residues: 1123 helix: 3.43 (0.19), residues: 721 sheet: -0.94 (0.49), residues: 93 loop : -0.20 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 472 HIS 0.008 0.001 HIS B 166 PHE 0.008 0.001 PHE D 120 TYR 0.014 0.001 TYR C 181 ARG 0.003 0.000 ARG B 383 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 618) hydrogen bonds : angle 3.43325 ( 1833) covalent geometry : bond 0.00245 ( 9063) covalent geometry : angle 0.45959 (12331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8419.01 seconds wall clock time: 148 minutes 11.21 seconds (8891.21 seconds total)