Starting phenix.real_space_refine on Thu Mar 13 23:52:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4l_31715/03_2025/7v4l_31715.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4l_31715/03_2025/7v4l_31715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v4l_31715/03_2025/7v4l_31715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4l_31715/03_2025/7v4l_31715.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4l_31715/03_2025/7v4l_31715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4l_31715/03_2025/7v4l_31715.cif" } resolution = 3.4 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= -0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5980 2.51 5 N 1530 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9345 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "C" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "D" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Time building chain proxies: 7.72, per 1000 atoms: 0.83 Number of scatterers: 9345 At special positions: 0 Unit cell: (117.665, 120.19, 61.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1780 8.00 N 1530 7.00 C 5980 6.00 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: 2.47 Conformation dependent library (CDL) restraints added in 1.0 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 19 sheets defined 23.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.706A pdb=" N GLY A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 215 through 228 removed outlier: 4.460A pdb=" N LEU A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.913A pdb=" N ALA A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.516A pdb=" N GLY B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.559A pdb=" N ASP B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 228 removed outlier: 3.976A pdb=" N LEU B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.588A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 183 " --> pdb=" O CYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 228 removed outlier: 3.559A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG C 223 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.712A pdb=" N THR C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.710A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 183 " --> pdb=" O CYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.180A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 223 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.718A pdb=" N THR D 350 " --> pdb=" O MET D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.636A pdb=" N VAL E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY E 183 " --> pdb=" O CYS E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 228 removed outlier: 4.180A pdb=" N GLY E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 350 removed outlier: 3.526A pdb=" N THR E 350 " --> pdb=" O MET E 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.803A pdb=" N ALA A 76 " --> pdb=" O MET A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.071A pdb=" N SER A 205 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.860A pdb=" N GLN A 130 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.605A pdb=" N ALA B 76 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 38 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 32 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N SER B 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY E 191 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN E 130 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR E 126 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER E 205 " --> pdb=" O TYR E 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.605A pdb=" N ALA B 76 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 38 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 32 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N SER B 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY E 191 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN E 130 " --> pdb=" O PHE E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.534A pdb=" N TYR B 132 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 130 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 133 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 40 removed outlier: 6.320A pdb=" N ILE C 20 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 90 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU C 22 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.695A pdb=" N GLY C 188 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 132 " --> pdb=" O TRP C 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 130 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.695A pdb=" N GLY C 188 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 132 " --> pdb=" O TRP C 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 130 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 33 through 40 removed outlier: 6.190A pdb=" N ILE D 20 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL D 90 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLU D 22 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.725A pdb=" N TYR D 132 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.725A pdb=" N TYR D 132 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.085A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP E 93 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR E 95 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU E 72 " --> pdb=" O TYR E 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 133 through 136 323 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1677 1.33 - 1.45: 2459 1.45 - 1.57: 5334 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9560 Sorted by residual: bond pdb=" C ASP C 339 " pdb=" N PRO C 340 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.08e-02 8.57e+03 1.36e+01 bond pdb=" C ASP E 339 " pdb=" N PRO E 340 " ideal model delta sigma weight residual 1.336 1.374 -0.039 1.08e-02 8.57e+03 1.27e+01 bond pdb=" CA ASP C 339 " pdb=" C ASP C 339 " ideal model delta sigma weight residual 1.522 1.564 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" CA ASP B 339 " pdb=" C ASP B 339 " ideal model delta sigma weight residual 1.521 1.558 -0.037 1.32e-02 5.74e+03 8.06e+00 bond pdb=" C ASP B 339 " pdb=" O ASP B 339 " ideal model delta sigma weight residual 1.246 1.221 0.025 9.20e-03 1.18e+04 7.67e+00 ... (remaining 9555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 12433 1.84 - 3.67: 427 3.67 - 5.51: 67 5.51 - 7.35: 21 7.35 - 9.18: 7 Bond angle restraints: 12955 Sorted by residual: angle pdb=" N LYS E 255 " pdb=" CA LYS E 255 " pdb=" C LYS E 255 " ideal model delta sigma weight residual 112.23 103.05 9.18 1.26e+00 6.30e-01 5.31e+01 angle pdb=" N LYS D 255 " pdb=" CA LYS D 255 " pdb=" C LYS D 255 " ideal model delta sigma weight residual 112.23 104.18 8.05 1.26e+00 6.30e-01 4.08e+01 angle pdb=" N ASN B 349 " pdb=" CA ASN B 349 " pdb=" C ASN B 349 " ideal model delta sigma weight residual 110.55 102.31 8.24 1.35e+00 5.49e-01 3.73e+01 angle pdb=" N ALA B 348 " pdb=" CA ALA B 348 " pdb=" C ALA B 348 " ideal model delta sigma weight residual 113.28 106.87 6.41 1.22e+00 6.72e-01 2.76e+01 angle pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" C ILE A 352 " ideal model delta sigma weight residual 109.37 116.17 -6.80 1.35e+00 5.49e-01 2.54e+01 ... (remaining 12950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4994 16.73 - 33.47: 544 33.47 - 50.20: 120 50.20 - 66.94: 37 66.94 - 83.67: 5 Dihedral angle restraints: 5700 sinusoidal: 2275 harmonic: 3425 Sorted by residual: dihedral pdb=" C ILE A 352 " pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" CB ILE A 352 " ideal model delta harmonic sigma weight residual -122.00 -133.91 11.91 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CA ARG A 38 " pdb=" C ARG A 38 " pdb=" N THR A 39 " pdb=" CA THR A 39 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CA ILE A 352 " pdb=" CB ILE A 352 " ideal model delta harmonic sigma weight residual 123.40 132.55 -9.15 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1162 0.068 - 0.136: 208 0.136 - 0.204: 34 0.204 - 0.272: 4 0.272 - 0.340: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA THR C 351 " pdb=" N THR C 351 " pdb=" C THR C 351 " pdb=" CB THR C 351 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE A 352 " pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CB ILE A 352 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ARG B 258 " pdb=" N ARG B 258 " pdb=" C ARG B 258 " pdb=" CB ARG B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1407 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 339 " 0.074 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 340 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 103 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 194 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 195 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " 0.032 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 197 2.66 - 3.22: 9031 3.22 - 3.78: 14294 3.78 - 4.34: 18893 4.34 - 4.90: 31070 Nonbonded interactions: 73485 Sorted by model distance: nonbonded pdb=" NH1 ARG B 169 " pdb=" OD1 ASP B 173 " model vdw 2.102 3.120 nonbonded pdb=" NH1 ARG C 169 " pdb=" OD1 ASP C 173 " model vdw 2.104 3.120 nonbonded pdb=" OE2 GLU D 22 " pdb=" OG SER D 35 " model vdw 2.148 3.040 nonbonded pdb=" OE2 GLU B 22 " pdb=" OG SER B 35 " model vdw 2.154 3.040 nonbonded pdb=" OE2 GLU C 22 " pdb=" OG SER C 35 " model vdw 2.180 3.040 ... (remaining 73480 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 143.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.990 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 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 : 0.005 0.049 9560 Z= 0.295 Angle : 0.817 9.185 12955 Z= 0.475 Chirality : 0.056 0.340 1410 Planarity : 0.007 0.114 1640 Dihedral : 15.200 83.670 3500 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.84 % Favored : 90.62 % Rotamer: Outliers : 3.71 % Allowed : 1.56 % Favored : 94.73 % Cbeta Deviations : 0.09 % 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: -2.60 (0.25), residues: 1120 helix: -0.22 (0.32), residues: 253 sheet: -2.45 (0.25), residues: 359 loop : -1.82 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 53 HIS 0.004 0.001 HIS C 175 PHE 0.014 0.002 PHE C 200 TYR 0.021 0.002 TYR A 132 ARG 0.009 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.5582 (m-10) cc_final: 0.4857 (m-10) REVERT: A 55 TYR cc_start: 0.6694 (p90) cc_final: 0.6013 (p90) REVERT: A 197 GLN cc_start: 0.7203 (mp10) cc_final: 0.6578 (mp10) REVERT: B 55 TYR cc_start: 0.6776 (p90) cc_final: 0.6086 (p90) REVERT: B 129 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6362 (mm-30) REVERT: C 55 TYR cc_start: 0.6574 (p90) cc_final: 0.5917 (p90) REVERT: D 55 TYR cc_start: 0.6712 (p90) cc_final: 0.5911 (p90) REVERT: E 55 TYR cc_start: 0.6758 (p90) cc_final: 0.6010 (p90) outliers start: 38 outliers final: 5 residues processed: 196 average time/residue: 0.1987 time to fit residues: 55.6503 Evaluate side-chains 151 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 256 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 ASN D 190 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.213610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.153546 restraints weight = 9353.360| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 4.08 r_work: 0.4157 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9560 Z= 0.406 Angle : 0.819 7.800 12955 Z= 0.434 Chirality : 0.054 0.205 1410 Planarity : 0.007 0.062 1640 Dihedral : 5.866 33.704 1280 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.45 % Favored : 89.46 % Rotamer: Outliers : 2.54 % Allowed : 12.00 % Favored : 85.46 % 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: -3.09 (0.24), residues: 1120 helix: -0.63 (0.31), residues: 264 sheet: -2.59 (0.26), residues: 340 loop : -2.34 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 53 HIS 0.005 0.002 HIS E 175 PHE 0.019 0.003 PHE C 200 TYR 0.029 0.003 TYR D 73 ARG 0.012 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7036 (p90) cc_final: 0.6234 (p90) REVERT: B 55 TYR cc_start: 0.7419 (p90) cc_final: 0.6580 (p90) REVERT: B 123 GLU cc_start: 0.6127 (tt0) cc_final: 0.5777 (tt0) REVERT: C 52 GLN cc_start: 0.7524 (mp10) cc_final: 0.6850 (tt0) REVERT: C 55 TYR cc_start: 0.7161 (p90) cc_final: 0.6362 (p90) REVERT: C 173 ASP cc_start: 0.5253 (m-30) cc_final: 0.5047 (m-30) REVERT: C 194 MET cc_start: 0.4186 (tpp) cc_final: 0.3690 (tpt) REVERT: D 55 TYR cc_start: 0.7204 (p90) cc_final: 0.6268 (p90) REVERT: D 197 GLN cc_start: 0.7620 (pp30) cc_final: 0.7263 (pp30) REVERT: D 257 MET cc_start: 0.5076 (tpt) cc_final: 0.4529 (mmm) REVERT: E 55 TYR cc_start: 0.7280 (p90) cc_final: 0.6347 (p90) REVERT: E 69 GLU cc_start: 0.6423 (tp30) cc_final: 0.6148 (tp30) REVERT: E 197 GLN cc_start: 0.7565 (pm20) cc_final: 0.6747 (pm20) REVERT: E 339 ASP cc_start: 0.6804 (t0) cc_final: 0.6460 (p0) outliers start: 26 outliers final: 20 residues processed: 177 average time/residue: 0.2360 time to fit residues: 62.9499 Evaluate side-chains 166 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.215945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.156110 restraints weight = 9178.814| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 4.19 r_work: 0.4148 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9560 Z= 0.222 Angle : 0.649 7.805 12955 Z= 0.341 Chirality : 0.048 0.189 1410 Planarity : 0.006 0.061 1640 Dihedral : 4.877 21.567 1271 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 2.15 % Allowed : 14.73 % Favored : 83.12 % 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: -2.76 (0.24), residues: 1120 helix: -0.19 (0.31), residues: 264 sheet: -2.57 (0.25), residues: 357 loop : -2.05 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 53 HIS 0.003 0.001 HIS D 175 PHE 0.017 0.002 PHE D 200 TYR 0.016 0.002 TYR A 132 ARG 0.004 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7035 (p90) cc_final: 0.6576 (p90) REVERT: B 55 TYR cc_start: 0.7367 (p90) cc_final: 0.6508 (p90) REVERT: B 123 GLU cc_start: 0.5805 (tt0) cc_final: 0.5200 (mt-10) REVERT: B 338 MET cc_start: 0.5288 (tpp) cc_final: 0.4724 (tpt) REVERT: D 55 TYR cc_start: 0.7272 (p90) cc_final: 0.6344 (p90) REVERT: D 197 GLN cc_start: 0.7435 (pp30) cc_final: 0.7086 (pp30) REVERT: D 257 MET cc_start: 0.5167 (tpt) cc_final: 0.4607 (mmm) REVERT: E 55 TYR cc_start: 0.7208 (p90) cc_final: 0.6231 (p90) REVERT: E 69 GLU cc_start: 0.6335 (tp30) cc_final: 0.6001 (tp30) REVERT: E 197 GLN cc_start: 0.7474 (pm20) cc_final: 0.6686 (pm20) REVERT: E 339 ASP cc_start: 0.6742 (t0) cc_final: 0.6435 (p0) outliers start: 22 outliers final: 16 residues processed: 174 average time/residue: 0.3008 time to fit residues: 79.8532 Evaluate side-chains 166 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 230 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 45 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.213414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.153169 restraints weight = 9216.497| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 4.30 r_work: 0.4124 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9560 Z= 0.247 Angle : 0.664 8.333 12955 Z= 0.347 Chirality : 0.049 0.193 1410 Planarity : 0.006 0.059 1640 Dihedral : 4.918 27.485 1270 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.20 % Favored : 90.71 % Rotamer: Outliers : 3.32 % Allowed : 16.00 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.83 (0.24), residues: 1120 helix: -0.24 (0.31), residues: 265 sheet: -2.59 (0.25), residues: 348 loop : -2.15 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 53 HIS 0.004 0.001 HIS D 175 PHE 0.018 0.002 PHE A 200 TYR 0.019 0.002 TYR E 126 ARG 0.005 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7428 (p90) cc_final: 0.6614 (p90) REVERT: A 180 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6805 (mp) REVERT: A 197 GLN cc_start: 0.7737 (mp10) cc_final: 0.7262 (mp10) REVERT: B 55 TYR cc_start: 0.7399 (p90) cc_final: 0.6578 (p90) REVERT: B 69 GLU cc_start: 0.6220 (tp30) cc_final: 0.5908 (tp30) REVERT: B 123 GLU cc_start: 0.5792 (tt0) cc_final: 0.5220 (mt-10) REVERT: B 173 ASP cc_start: 0.5134 (m-30) cc_final: 0.4861 (m-30) REVERT: B 180 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7094 (mm) REVERT: B 338 MET cc_start: 0.5412 (tpp) cc_final: 0.4819 (tpt) REVERT: C 52 GLN cc_start: 0.7374 (mp10) cc_final: 0.6727 (tt0) REVERT: C 129 GLU cc_start: 0.7154 (mp0) cc_final: 0.6903 (mp0) REVERT: C 201 GLN cc_start: 0.7290 (mm-40) cc_final: 0.7000 (mm-40) REVERT: D 55 TYR cc_start: 0.7309 (p90) cc_final: 0.6453 (p90) REVERT: D 192 GLU cc_start: 0.6258 (mm-30) cc_final: 0.6013 (mm-30) REVERT: D 197 GLN cc_start: 0.7566 (pp30) cc_final: 0.7285 (pp30) REVERT: D 257 MET cc_start: 0.5282 (tpt) cc_final: 0.4747 (mmm) REVERT: E 69 GLU cc_start: 0.6345 (tp30) cc_final: 0.6007 (tp30) REVERT: E 197 GLN cc_start: 0.7518 (pm20) cc_final: 0.6732 (pm20) outliers start: 34 outliers final: 20 residues processed: 182 average time/residue: 0.1723 time to fit residues: 46.7608 Evaluate side-chains 175 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.211000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.152675 restraints weight = 9398.529| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 4.23 r_work: 0.4098 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9560 Z= 0.292 Angle : 0.727 12.283 12955 Z= 0.376 Chirality : 0.050 0.211 1410 Planarity : 0.006 0.058 1640 Dihedral : 5.061 17.999 1270 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 3.41 % Allowed : 16.88 % Favored : 79.71 % 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: -2.96 (0.24), residues: 1120 helix: -0.45 (0.31), residues: 265 sheet: -2.66 (0.24), residues: 353 loop : -2.14 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 53 HIS 0.006 0.001 HIS D 175 PHE 0.018 0.002 PHE A 200 TYR 0.022 0.002 TYR A 132 ARG 0.005 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7420 (p90) cc_final: 0.6646 (p90) REVERT: A 180 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6805 (mp) REVERT: A 197 GLN cc_start: 0.7781 (mp10) cc_final: 0.7246 (mp10) REVERT: B 55 TYR cc_start: 0.7421 (p90) cc_final: 0.6650 (p90) REVERT: B 123 GLU cc_start: 0.5867 (tt0) cc_final: 0.5302 (mt-10) REVERT: B 126 TYR cc_start: 0.5924 (m-80) cc_final: 0.5685 (m-80) REVERT: B 338 MET cc_start: 0.5413 (tpp) cc_final: 0.4852 (tpt) REVERT: C 52 GLN cc_start: 0.7477 (mp10) cc_final: 0.6948 (tt0) REVERT: D 55 TYR cc_start: 0.7348 (p90) cc_final: 0.6512 (p90) REVERT: D 257 MET cc_start: 0.5367 (tpt) cc_final: 0.4777 (mmm) REVERT: E 55 TYR cc_start: 0.7326 (p90) cc_final: 0.6346 (p90) REVERT: E 69 GLU cc_start: 0.6365 (tp30) cc_final: 0.5970 (tp30) REVERT: E 197 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: E 222 GLU cc_start: 0.6163 (OUTLIER) cc_final: 0.5506 (mp0) outliers start: 35 outliers final: 22 residues processed: 184 average time/residue: 0.1694 time to fit residues: 46.2467 Evaluate side-chains 175 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 1 optimal weight: 0.3980 chunk 81 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.209902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.150746 restraints weight = 9357.411| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 4.09 r_work: 0.4099 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9560 Z= 0.291 Angle : 0.719 9.532 12955 Z= 0.374 Chirality : 0.050 0.213 1410 Planarity : 0.006 0.058 1640 Dihedral : 5.121 17.667 1270 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 4.98 % Allowed : 16.98 % Favored : 78.05 % 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: -3.01 (0.24), residues: 1120 helix: -0.54 (0.31), residues: 265 sheet: -2.63 (0.25), residues: 335 loop : -2.24 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 53 HIS 0.005 0.001 HIS D 175 PHE 0.019 0.002 PHE A 200 TYR 0.021 0.002 TYR A 132 ARG 0.005 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 TRP cc_start: 0.5933 (p90) cc_final: 0.5719 (p90) REVERT: A 55 TYR cc_start: 0.7414 (p90) cc_final: 0.6689 (p90) REVERT: A 129 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: A 180 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6872 (mp) REVERT: B 55 TYR cc_start: 0.7462 (p90) cc_final: 0.6743 (p90) REVERT: B 123 GLU cc_start: 0.5971 (tt0) cc_final: 0.5371 (mt-10) REVERT: B 338 MET cc_start: 0.5476 (tpp) cc_final: 0.4856 (tpt) REVERT: C 52 GLN cc_start: 0.7393 (mp10) cc_final: 0.6836 (tt0) REVERT: D 55 TYR cc_start: 0.7332 (p90) cc_final: 0.6486 (p90) REVERT: D 257 MET cc_start: 0.5441 (tpt) cc_final: 0.4857 (mmm) REVERT: E 55 TYR cc_start: 0.7342 (p90) cc_final: 0.6402 (p90) REVERT: E 69 GLU cc_start: 0.6460 (tp30) cc_final: 0.6074 (tp30) REVERT: E 197 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: E 222 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5559 (mp0) REVERT: E 339 ASP cc_start: 0.6709 (t0) cc_final: 0.6482 (p0) outliers start: 51 outliers final: 33 residues processed: 186 average time/residue: 0.1677 time to fit residues: 47.0279 Evaluate side-chains 180 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 0.3980 chunk 44 optimal weight: 20.0000 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.215386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.156647 restraints weight = 9292.293| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 4.21 r_work: 0.4159 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9560 Z= 0.202 Angle : 0.656 9.349 12955 Z= 0.340 Chirality : 0.047 0.213 1410 Planarity : 0.006 0.060 1640 Dihedral : 4.606 16.192 1270 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.90 % Allowed : 19.12 % Favored : 76.98 % 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: -2.66 (0.24), residues: 1120 helix: -0.14 (0.31), residues: 265 sheet: -2.46 (0.24), residues: 352 loop : -2.02 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 53 HIS 0.003 0.001 HIS D 175 PHE 0.018 0.001 PHE A 200 TYR 0.014 0.001 TYR E 176 ARG 0.003 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 25 TRP cc_start: 0.5842 (p90) cc_final: 0.5634 (p90) REVERT: A 55 TYR cc_start: 0.7342 (p90) cc_final: 0.6585 (p90) REVERT: A 129 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 197 GLN cc_start: 0.7625 (mp10) cc_final: 0.7170 (mp10) REVERT: B 55 TYR cc_start: 0.7352 (p90) cc_final: 0.6630 (p90) REVERT: B 123 GLU cc_start: 0.5796 (tt0) cc_final: 0.5185 (mt-10) REVERT: B 338 MET cc_start: 0.5524 (tpp) cc_final: 0.4959 (tpt) REVERT: C 52 GLN cc_start: 0.7306 (mp10) cc_final: 0.6863 (tt0) REVERT: C 55 TYR cc_start: 0.7443 (p90) cc_final: 0.6665 (p90) REVERT: C 129 GLU cc_start: 0.7114 (mp0) cc_final: 0.6484 (mp0) REVERT: C 201 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6895 (mm-40) REVERT: D 55 TYR cc_start: 0.7264 (p90) cc_final: 0.6464 (p90) REVERT: D 192 GLU cc_start: 0.6137 (mm-30) cc_final: 0.5776 (mm-30) REVERT: D 197 GLN cc_start: 0.7500 (pp30) cc_final: 0.7280 (pp30) REVERT: D 199 GLU cc_start: 0.7916 (tt0) cc_final: 0.7587 (tm-30) REVERT: D 257 MET cc_start: 0.5478 (tpt) cc_final: 0.4870 (mmm) REVERT: E 197 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6757 (pm20) outliers start: 40 outliers final: 26 residues processed: 179 average time/residue: 0.1685 time to fit residues: 44.8535 Evaluate side-chains 174 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 197 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.211409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.152182 restraints weight = 9599.954| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 3.49 r_work: 0.4086 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9560 Z= 0.284 Angle : 0.721 9.493 12955 Z= 0.376 Chirality : 0.050 0.225 1410 Planarity : 0.006 0.062 1640 Dihedral : 4.941 16.919 1270 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.61 % Allowed : 19.32 % Favored : 77.07 % 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: -2.84 (0.24), residues: 1120 helix: -0.37 (0.31), residues: 263 sheet: -2.48 (0.25), residues: 339 loop : -2.19 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 53 HIS 0.004 0.001 HIS D 175 PHE 0.017 0.002 PHE A 200 TYR 0.018 0.002 TYR A 132 ARG 0.005 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7368 (p90) cc_final: 0.6592 (p90) REVERT: A 129 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 180 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6820 (mp) REVERT: B 55 TYR cc_start: 0.7435 (p90) cc_final: 0.6657 (p90) REVERT: B 123 GLU cc_start: 0.5700 (tt0) cc_final: 0.5168 (mt-10) REVERT: B 338 MET cc_start: 0.5471 (tpp) cc_final: 0.4847 (tpt) REVERT: C 52 GLN cc_start: 0.7412 (mp10) cc_final: 0.6858 (tt0) REVERT: C 55 TYR cc_start: 0.7515 (p90) cc_final: 0.6727 (p90) REVERT: D 257 MET cc_start: 0.5510 (tpt) cc_final: 0.4919 (mmm) REVERT: E 55 TYR cc_start: 0.7340 (p90) cc_final: 0.6412 (p90) REVERT: E 197 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6786 (pm20) outliers start: 37 outliers final: 30 residues processed: 167 average time/residue: 0.1634 time to fit residues: 41.3592 Evaluate side-chains 170 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 96 optimal weight: 0.0050 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.214643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.156412 restraints weight = 9304.786| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 4.31 r_work: 0.4163 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9560 Z= 0.208 Angle : 0.668 11.205 12955 Z= 0.346 Chirality : 0.047 0.225 1410 Planarity : 0.006 0.076 1640 Dihedral : 4.538 15.988 1270 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.64 % Rotamer: Outliers : 3.80 % Allowed : 20.29 % Favored : 75.90 % 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: -2.55 (0.24), residues: 1120 helix: -0.04 (0.31), residues: 263 sheet: -2.32 (0.26), residues: 339 loop : -2.04 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 53 HIS 0.002 0.001 HIS B 175 PHE 0.016 0.001 PHE A 200 TYR 0.013 0.001 TYR E 73 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7359 (p90) cc_final: 0.6679 (p90) REVERT: A 129 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 55 TYR cc_start: 0.7347 (p90) cc_final: 0.6655 (p90) REVERT: B 123 GLU cc_start: 0.5655 (tt0) cc_final: 0.5092 (mt-10) REVERT: B 338 MET cc_start: 0.5469 (tpp) cc_final: 0.4897 (tpt) REVERT: C 52 GLN cc_start: 0.7373 (mp10) cc_final: 0.6845 (tt0) REVERT: C 55 TYR cc_start: 0.7462 (p90) cc_final: 0.6668 (p90) REVERT: C 129 GLU cc_start: 0.7048 (mp0) cc_final: 0.6443 (mp0) REVERT: C 201 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6967 (mm-40) REVERT: D 197 GLN cc_start: 0.7514 (pp30) cc_final: 0.7292 (pp30) REVERT: D 257 MET cc_start: 0.5489 (tpt) cc_final: 0.4955 (mmm) REVERT: E 197 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6737 (pm20) outliers start: 39 outliers final: 29 residues processed: 169 average time/residue: 0.1774 time to fit residues: 44.4939 Evaluate side-chains 167 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.210383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.150249 restraints weight = 9607.135| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 3.58 r_work: 0.4090 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9560 Z= 0.320 Angle : 0.757 10.753 12955 Z= 0.395 Chirality : 0.050 0.225 1410 Planarity : 0.007 0.082 1640 Dihedral : 5.102 17.977 1270 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.38 % Favored : 90.54 % Rotamer: Outliers : 3.41 % Allowed : 20.68 % Favored : 75.90 % 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: -2.91 (0.24), residues: 1120 helix: -0.48 (0.31), residues: 263 sheet: -2.47 (0.26), residues: 347 loop : -2.22 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 53 HIS 0.004 0.001 HIS E 175 PHE 0.016 0.002 PHE A 200 TYR 0.022 0.002 TYR A 132 ARG 0.006 0.001 ARG E 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7463 (p90) cc_final: 0.6777 (p90) REVERT: A 129 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 180 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6864 (mp) REVERT: B 55 TYR cc_start: 0.7452 (p90) cc_final: 0.6731 (p90) REVERT: B 123 GLU cc_start: 0.5711 (tt0) cc_final: 0.5198 (mt-10) REVERT: B 201 GLN cc_start: 0.6909 (mm-40) cc_final: 0.6657 (mm-40) REVERT: B 338 MET cc_start: 0.5556 (tpp) cc_final: 0.4899 (tpt) REVERT: C 52 GLN cc_start: 0.7483 (mp10) cc_final: 0.6773 (tt0) REVERT: C 55 TYR cc_start: 0.7521 (p90) cc_final: 0.6716 (p90) REVERT: D 257 MET cc_start: 0.5575 (tpt) cc_final: 0.5119 (mmm) REVERT: E 55 TYR cc_start: 0.7331 (p90) cc_final: 0.6409 (p90) REVERT: E 197 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6910 (pm20) outliers start: 35 outliers final: 28 residues processed: 168 average time/residue: 0.1633 time to fit residues: 41.3961 Evaluate side-chains 167 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 197 GLN Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.209490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.150742 restraints weight = 9545.060| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.44 r_work: 0.4080 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9560 Z= 0.308 Angle : 0.755 10.392 12955 Z= 0.394 Chirality : 0.050 0.219 1410 Planarity : 0.007 0.085 1640 Dihedral : 5.135 17.955 1270 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 3.12 % Allowed : 20.98 % Favored : 75.90 % 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: -2.98 (0.24), residues: 1120 helix: -0.57 (0.31), residues: 263 sheet: -2.48 (0.26), residues: 342 loop : -2.29 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 53 HIS 0.004 0.001 HIS D 175 PHE 0.016 0.002 PHE A 200 TYR 0.022 0.002 TYR A 132 ARG 0.006 0.001 ARG E 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6425.21 seconds wall clock time: 113 minutes 58.81 seconds (6838.81 seconds total)