Starting phenix.real_space_refine on Sat Sep 28 01:36:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/09_2024/8dp5_27630.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/09_2024/8dp5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/09_2024/8dp5_27630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/09_2024/8dp5_27630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/09_2024/8dp5_27630.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dp5_27630/09_2024/8dp5_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-5461/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: 8.73, per 1000 atoms: 0.49 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: 4.29 Conformation dependent library (CDL) restraints added in 1.5 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: 1.31 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: 5.71 Time building geometry restraints manager: 5.18 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: 1.800 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: 0.300 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.940 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.170 ------------------------------------------------------------------------------- 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= 0.862 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.317 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: 0.6131 time to fit residues: 106.0928 Evaluate side-chains 64 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2504 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= 0.245 Angle : 0.653 7.363 12331 Z= 0.352 Chirality : 0.038 0.142 1384 Planarity : 0.006 0.062 1598 Dihedral : 5.293 31.746 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 ASP cc_start: 0.6924 (t0) cc_final: 0.6669 (t0) REVERT: B 207 LYS cc_start: 0.7415 (tttt) cc_final: 0.7195 (tttp) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.5961 time to fit residues: 56.9854 Evaluate side-chains 61 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 56 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9063 Z= 0.248 Angle : 0.578 6.681 12331 Z= 0.304 Chirality : 0.037 0.141 1384 Planarity : 0.005 0.052 1598 Dihedral : 4.905 36.241 1250 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.22 % Allowed : 3.89 % Favored : 95.89 % 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: 1.88 (0.25), residues: 1123 helix: 2.29 (0.19), residues: 716 sheet: -0.84 (0.52), residues: 99 loop : -0.52 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.008 0.001 HIS B 166 PHE 0.012 0.001 PHE D 120 TYR 0.018 0.002 TYR C 127 ARG 0.003 0.000 ARG A 156 *********************** 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 62 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: B 171 PHE cc_start: 0.8216 (m-80) cc_final: 0.7991 (m-80) REVERT: B 175 ASP cc_start: 0.6951 (t0) cc_final: 0.6722 (t0) outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 0.6867 time to fit residues: 55.3805 Evaluate side-chains 55 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9063 Z= 0.162 Angle : 0.519 6.772 12331 Z= 0.268 Chirality : 0.035 0.137 1384 Planarity : 0.005 0.052 1598 Dihedral : 4.544 35.187 1250 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.25), residues: 1123 helix: 2.82 (0.19), residues: 716 sheet: -0.73 (0.53), residues: 93 loop : -0.45 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.006 0.001 HIS C 166 PHE 0.009 0.001 PHE D 120 TYR 0.014 0.001 TYR C 127 ARG 0.002 0.000 ARG A 156 *********************** 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 68 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.375 Fit side-chains REVERT: A 196 ASP cc_start: 0.7452 (t0) cc_final: 0.7204 (t0) REVERT: B 175 ASP cc_start: 0.6881 (t0) cc_final: 0.6626 (t70) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.6232 time to fit residues: 55.3506 Evaluate side-chains 58 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9063 Z= 0.220 Angle : 0.513 6.348 12331 Z= 0.263 Chirality : 0.035 0.134 1384 Planarity : 0.005 0.049 1598 Dihedral : 4.436 37.026 1250 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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 (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: 2.62 (0.25), residues: 1123 helix: 2.96 (0.19), residues: 718 sheet: -0.90 (0.51), residues: 93 loop : -0.41 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.011 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 B 438 *********************** 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 58 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7462 (t0) cc_final: 0.7170 (t0) outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.6783 time to fit residues: 51.3331 Evaluate side-chains 56 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9063 Z= 0.302 Angle : 0.546 5.914 12331 Z= 0.282 Chirality : 0.036 0.138 1384 Planarity : 0.005 0.050 1598 Dihedral : 4.502 41.220 1250 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % 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: 2.40 (0.25), residues: 1123 helix: 2.83 (0.19), residues: 717 sheet: -1.10 (0.49), residues: 99 loop : -0.55 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.011 0.001 HIS B 166 PHE 0.015 0.001 PHE D 120 TYR 0.017 0.002 TYR A 188 ARG 0.003 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7531 (t0) cc_final: 0.7253 (t0) outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.6160 time to fit residues: 53.2498 Evaluate side-chains 61 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 12 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3757 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= 0.197 Angle : 0.497 5.795 12331 Z= 0.255 Chirality : 0.034 0.132 1384 Planarity : 0.005 0.045 1598 Dihedral : 4.365 39.970 1250 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.11 % Allowed : 6.49 % 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 (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: 2.64 (0.25), residues: 1123 helix: 3.00 (0.19), residues: 719 sheet: -0.92 (0.51), residues: 93 loop : -0.48 (0.34), residues: 311 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 0.013 0.001 PHE B 171 TYR 0.013 0.001 TYR C 127 ARG 0.003 0.000 ARG B 438 *********************** 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 66 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7513 (t0) cc_final: 0.7229 (t0) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.6286 time to fit residues: 54.1076 Evaluate side-chains 64 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3912 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= 0.162 Angle : 0.484 5.781 12331 Z= 0.245 Chirality : 0.034 0.129 1384 Planarity : 0.005 0.044 1598 Dihedral : 4.195 37.451 1250 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 7.35 % 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 (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: 2.87 (0.25), residues: 1123 helix: 3.20 (0.19), residues: 718 sheet: -0.94 (0.50), residues: 93 loop : -0.39 (0.35), residues: 312 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 0.009 0.001 PHE B 171 TYR 0.013 0.001 TYR C 127 ARG 0.007 0.000 ARG B 438 *********************** 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 66 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7504 (t0) cc_final: 0.7245 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.6210 time to fit residues: 53.5762 Evaluate side-chains 63 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3950 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= 0.199 Angle : 0.485 5.722 12331 Z= 0.246 Chirality : 0.034 0.133 1384 Planarity : 0.005 0.043 1598 Dihedral : 4.197 38.044 1250 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.22 % 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: 2.86 (0.25), residues: 1123 helix: 3.19 (0.19), residues: 720 sheet: -0.97 (0.50), residues: 99 loop : -0.38 (0.35), residues: 304 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 0.010 0.001 PHE D 120 TYR 0.019 0.001 TYR C 181 ARG 0.006 0.000 ARG B 438 *********************** 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 fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7519 (t0) cc_final: 0.7260 (t0) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.6379 time to fit residues: 54.3855 Evaluate side-chains 64 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4030 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= 0.241 Angle : 0.501 5.792 12331 Z= 0.255 Chirality : 0.035 0.134 1384 Planarity : 0.005 0.043 1598 Dihedral : 4.217 39.849 1250 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.11 % Allowed : 7.78 % Favored : 92.11 % 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: 2.77 (0.25), residues: 1123 helix: 3.13 (0.18), residues: 721 sheet: -1.04 (0.50), residues: 99 loop : -0.45 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 472 HIS 0.009 0.001 HIS B 166 PHE 0.012 0.001 PHE D 120 TYR 0.017 0.001 TYR C 181 ARG 0.005 0.000 ARG B 438 ********************** 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 fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 ASP cc_start: 0.7486 (t0) cc_final: 0.7222 (t0) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.6384 time to fit residues: 51.9158 Evaluate side-chains 62 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.139375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100416 restraints weight = 36992.141| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.81 r_work: 0.3214 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4111 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= 0.145 Angle : 0.466 5.660 12331 Z= 0.235 Chirality : 0.033 0.128 1384 Planarity : 0.004 0.044 1598 Dihedral : 4.090 39.797 1250 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.22 % 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: 3.02 (0.26), residues: 1123 helix: 3.30 (0.19), residues: 722 sheet: -0.98 (0.50), residues: 93 loop : -0.31 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 472 HIS 0.008 0.001 HIS B 166 PHE 0.007 0.001 PHE D 120 TYR 0.012 0.001 TYR B 188 ARG 0.004 0.000 ARG B 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.65 seconds wall clock time: 62 minutes 49.12 seconds (3769.12 seconds total)