Starting phenix.real_space_refine on Wed Sep 17 15:13:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4l_31715/09_2025/7v4l_31715.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4l_31715/09_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_31715/09_2025/7v4l_31715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4l_31715/09_2025/7v4l_31715.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4l_31715/09_2025/7v4l_31715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4l_31715/09_2025/7v4l_31715.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.40, per 1000 atoms: 0.26 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: 0.82 Conformation dependent library (CDL) restraints added in 332.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 1.34 Time building geometry restraints manager: 1.08 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: 0.01 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: 12.770 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.810 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- 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= 0.237 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (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 ARG 0.009 0.001 ARG B 169 TYR 0.021 0.002 TYR A 132 PHE 0.014 0.002 PHE C 200 TRP 0.034 0.002 TRP D 53 HIS 0.004 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9560) covalent geometry : angle 0.81669 (12955) hydrogen bonds : bond 0.18865 ( 294) hydrogen bonds : angle 8.66190 ( 903) *********************** 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 : 0.334 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: 0.0861 time to fit residues: 24.3654 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 : 0.292 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- 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 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.219312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.159149 restraints weight = 9217.230| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 4.14 r_work: 0.4222 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9560 Z= 0.172 Angle : 0.717 7.802 12955 Z= 0.377 Chirality : 0.050 0.167 1410 Planarity : 0.006 0.063 1640 Dihedral : 5.340 39.107 1280 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.39 % Favored : 91.52 % Rotamer: Outliers : 1.56 % Allowed : 11.02 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.24), residues: 1120 helix: -0.06 (0.32), residues: 264 sheet: -2.51 (0.25), residues: 350 loop : -2.05 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 169 TYR 0.026 0.002 TYR D 73 PHE 0.021 0.002 PHE D 200 TRP 0.024 0.002 TRP D 53 HIS 0.004 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9560) covalent geometry : angle 0.71667 (12955) hydrogen bonds : bond 0.05649 ( 294) hydrogen bonds : angle 6.20891 ( 903) *********************** 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 177 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.6192 (m-10) cc_final: 0.5779 (m-10) REVERT: A 55 TYR cc_start: 0.6969 (p90) cc_final: 0.6506 (p90) REVERT: A 197 GLN cc_start: 0.7589 (mp10) cc_final: 0.6937 (mp10) REVERT: B 55 TYR cc_start: 0.7383 (p90) cc_final: 0.6554 (p90) REVERT: B 123 GLU cc_start: 0.5893 (tt0) cc_final: 0.5230 (mt-10) REVERT: C 55 TYR cc_start: 0.7077 (p90) cc_final: 0.6224 (p90) REVERT: C 194 MET cc_start: 0.4135 (tpp) cc_final: 0.3644 (tpt) REVERT: D 55 TYR cc_start: 0.7090 (p90) cc_final: 0.6156 (p90) REVERT: D 197 GLN cc_start: 0.7367 (pp30) cc_final: 0.7002 (pp30) REVERT: D 257 MET cc_start: 0.5033 (tpt) cc_final: 0.4458 (mmm) REVERT: E 55 TYR cc_start: 0.7181 (p90) cc_final: 0.6242 (p90) REVERT: E 69 GLU cc_start: 0.6301 (tp30) cc_final: 0.6001 (tp30) REVERT: E 339 ASP cc_start: 0.6746 (t0) cc_final: 0.6427 (p0) outliers start: 16 outliers final: 14 residues processed: 173 average time/residue: 0.0743 time to fit residues: 19.3959 Evaluate side-chains 161 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASP 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 B residue 255 LYS Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 53 TRP 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 256 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 89 optimal weight: 0.0070 chunk 112 optimal weight: 3.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** 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** B 201 GLN 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 = 0.5119 r_free = 0.5119 target = 0.220798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.162861 restraints weight = 9286.029| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 3.96 r_work: 0.4238 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9560 Z= 0.147 Angle : 0.641 8.464 12955 Z= 0.337 Chirality : 0.048 0.190 1410 Planarity : 0.006 0.060 1640 Dihedral : 4.771 19.261 1271 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.32 % Favored : 92.59 % Rotamer: Outliers : 2.54 % Allowed : 13.46 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.24), residues: 1120 helix: -0.06 (0.31), residues: 264 sheet: -2.53 (0.25), residues: 348 loop : -1.97 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 169 TYR 0.017 0.002 TYR E 73 PHE 0.017 0.002 PHE A 200 TRP 0.023 0.001 TRP D 53 HIS 0.003 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9560) covalent geometry : angle 0.64067 (12955) hydrogen bonds : bond 0.05016 ( 294) hydrogen bonds : angle 5.87255 ( 903) *********************** 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 182 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.6252 (m-10) cc_final: 0.5819 (m-10) REVERT: A 55 TYR cc_start: 0.7305 (p90) cc_final: 0.6453 (p90) REVERT: B 55 TYR cc_start: 0.7327 (p90) cc_final: 0.6531 (p90) REVERT: B 123 GLU cc_start: 0.5996 (tt0) cc_final: 0.5583 (tt0) REVERT: B 180 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7113 (mm) REVERT: B 255 LYS cc_start: 0.5442 (OUTLIER) cc_final: 0.4896 (ptpt) REVERT: B 338 MET cc_start: 0.5703 (tpp) cc_final: 0.5033 (tpt) REVERT: C 52 GLN cc_start: 0.7287 (mp10) cc_final: 0.6794 (tt0) REVERT: C 55 TYR cc_start: 0.7102 (p90) cc_final: 0.6681 (p90) REVERT: C 201 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6953 (mm-40) REVERT: D 55 TYR cc_start: 0.7124 (p90) cc_final: 0.6207 (p90) REVERT: D 197 GLN cc_start: 0.7389 (pp30) cc_final: 0.7060 (pp30) REVERT: D 257 MET cc_start: 0.5129 (tpt) cc_final: 0.4552 (mmm) REVERT: E 55 TYR cc_start: 0.7193 (p90) cc_final: 0.6190 (p90) REVERT: E 69 GLU cc_start: 0.6327 (tp30) cc_final: 0.5966 (tp30) REVERT: E 197 GLN cc_start: 0.7430 (pm20) cc_final: 0.6635 (pm20) outliers start: 26 outliers final: 16 residues processed: 175 average time/residue: 0.0682 time to fit residues: 18.4648 Evaluate side-chains 167 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL 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 B residue 255 LYS 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 214 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** 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** ** E 130 GLN ** 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 = 0.5137 r_free = 0.5137 target = 0.222904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.162574 restraints weight = 9180.118| |-----------------------------------------------------------------------------| r_work (start): 0.4494 rms_B_bonded: 4.25 r_work: 0.4258 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.2268 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= 0.124 Angle : 0.611 8.550 12955 Z= 0.317 Chirality : 0.046 0.194 1410 Planarity : 0.006 0.060 1640 Dihedral : 4.520 25.578 1270 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 3.41 % Allowed : 14.24 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.24), residues: 1120 helix: 0.04 (0.31), residues: 264 sheet: -2.50 (0.25), residues: 349 loop : -1.81 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 258 TYR 0.018 0.001 TYR E 126 PHE 0.016 0.001 PHE D 200 TRP 0.020 0.001 TRP D 53 HIS 0.003 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9560) covalent geometry : angle 0.61051 (12955) hydrogen bonds : bond 0.04441 ( 294) hydrogen bonds : angle 5.60605 ( 903) *********************** 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 196 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.6247 (m-10) cc_final: 0.5763 (m-10) REVERT: A 55 TYR cc_start: 0.7266 (p90) cc_final: 0.6385 (p90) REVERT: A 90 VAL cc_start: 0.4865 (t) cc_final: 0.4661 (t) REVERT: A 180 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6723 (mp) REVERT: B 55 TYR cc_start: 0.7229 (p90) cc_final: 0.6438 (p90) REVERT: B 123 GLU cc_start: 0.5907 (tt0) cc_final: 0.5050 (mt-10) REVERT: B 194 MET cc_start: 0.3751 (tpp) cc_final: 0.3523 (tpp) REVERT: B 338 MET cc_start: 0.5771 (tpp) cc_final: 0.5142 (tpt) REVERT: C 52 GLN cc_start: 0.7268 (mp10) cc_final: 0.6820 (tt0) REVERT: D 55 TYR cc_start: 0.7113 (p90) cc_final: 0.6222 (p90) REVERT: D 197 GLN cc_start: 0.7329 (pp30) cc_final: 0.7041 (pp30) REVERT: D 257 MET cc_start: 0.5234 (tpt) cc_final: 0.4748 (mmm) REVERT: E 55 TYR cc_start: 0.7185 (p90) cc_final: 0.6228 (p90) REVERT: E 69 GLU cc_start: 0.6302 (tp30) cc_final: 0.5930 (tp30) REVERT: E 197 GLN cc_start: 0.7426 (pm20) cc_final: 0.6603 (pm20) REVERT: E 339 ASP cc_start: 0.6661 (t0) cc_final: 0.6428 (p0) outliers start: 35 outliers final: 23 residues processed: 186 average time/residue: 0.0701 time to fit residues: 19.8389 Evaluate side-chains 177 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN 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 199 GLU 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 22 GLU Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 202 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 19 ILE Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 224 ILE 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 67 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 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 87 ASN ** 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 = 0.5081 r_free = 0.5081 target = 0.216393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.157900 restraints weight = 9304.741| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 3.98 r_work: 0.4199 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9560 Z= 0.182 Angle : 0.704 12.250 12955 Z= 0.365 Chirality : 0.050 0.206 1410 Planarity : 0.006 0.061 1640 Dihedral : 4.905 18.224 1270 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.93 % Favored : 90.98 % Rotamer: Outliers : 3.80 % Allowed : 15.80 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.24), residues: 1120 helix: -0.36 (0.31), residues: 265 sheet: -2.56 (0.25), residues: 348 loop : -2.03 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 169 TYR 0.020 0.002 TYR A 132 PHE 0.017 0.002 PHE A 200 TRP 0.024 0.001 TRP D 53 HIS 0.006 0.001 HIS D 175 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9560) covalent geometry : angle 0.70364 (12955) hydrogen bonds : bond 0.05123 ( 294) hydrogen bonds : angle 6.00222 ( 903) *********************** 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 194 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7341 (p90) cc_final: 0.6539 (p90) REVERT: A 75 GLN cc_start: 0.6351 (pm20) cc_final: 0.5979 (mp10) REVERT: A 90 VAL cc_start: 0.4983 (t) cc_final: 0.4767 (t) REVERT: A 129 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 180 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6855 (mp) REVERT: A 197 GLN cc_start: 0.7720 (mp10) cc_final: 0.7240 (mp10) REVERT: B 55 TYR cc_start: 0.7339 (p90) cc_final: 0.6608 (p90) REVERT: B 123 GLU cc_start: 0.5927 (tt0) cc_final: 0.5593 (mt-10) REVERT: B 338 MET cc_start: 0.5907 (tpp) cc_final: 0.5249 (tpt) REVERT: C 52 GLN cc_start: 0.7398 (mp10) cc_final: 0.6927 (tt0) REVERT: D 55 TYR cc_start: 0.7170 (p90) cc_final: 0.6323 (p90) REVERT: D 197 GLN cc_start: 0.7572 (pp30) cc_final: 0.7362 (pp30) REVERT: D 222 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5726 (mp0) REVERT: D 257 MET cc_start: 0.5330 (tpt) cc_final: 0.4768 (mmm) REVERT: E 55 TYR cc_start: 0.7290 (p90) cc_final: 0.6367 (p90) REVERT: E 197 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: E 339 ASP cc_start: 0.6713 (t0) cc_final: 0.6495 (p0) outliers start: 39 outliers final: 22 residues processed: 181 average time/residue: 0.0744 time to fit residues: 20.0726 Evaluate side-chains 179 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 24 ILE Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 227 ILE 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 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 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: 7.9990 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 75 GLN ** 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 C 201 GLN D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.210531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.151996 restraints weight = 9501.320| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 4.21 r_work: 0.4085 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9560 Z= 0.185 Angle : 0.732 12.229 12955 Z= 0.379 Chirality : 0.050 0.210 1410 Planarity : 0.006 0.061 1640 Dihedral : 5.027 20.758 1270 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 3.71 % Allowed : 16.78 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.24), residues: 1120 helix: -0.56 (0.31), residues: 265 sheet: -2.62 (0.25), residues: 339 loop : -2.15 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 83 TYR 0.023 0.002 TYR A 132 PHE 0.019 0.002 PHE C 200 TRP 0.026 0.001 TRP D 53 HIS 0.006 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9560) covalent geometry : angle 0.73236 (12955) hydrogen bonds : bond 0.05363 ( 294) hydrogen bonds : angle 6.13303 ( 903) *********************** 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 192 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7424 (p90) cc_final: 0.6631 (p90) REVERT: A 197 GLN cc_start: 0.7798 (mp10) cc_final: 0.7254 (mp10) REVERT: B 55 TYR cc_start: 0.7447 (p90) cc_final: 0.6735 (p90) REVERT: B 126 TYR cc_start: 0.5735 (m-80) cc_final: 0.5485 (m-80) REVERT: B 338 MET cc_start: 0.5540 (tpp) cc_final: 0.4907 (tpt) REVERT: C 52 GLN cc_start: 0.7481 (mp10) cc_final: 0.6992 (tt0) REVERT: D 55 TYR cc_start: 0.7360 (p90) cc_final: 0.6463 (p90) REVERT: D 257 MET cc_start: 0.5412 (tpt) cc_final: 0.4789 (mmm) REVERT: E 197 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: E 339 ASP cc_start: 0.6665 (t0) cc_final: 0.6432 (p0) outliers start: 38 outliers final: 24 residues processed: 178 average time/residue: 0.0754 time to fit residues: 20.3302 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 : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE 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 C residue 6 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 222 GLU 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 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 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 97 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.210723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.151808 restraints weight = 9369.341| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.39 r_work: 0.4108 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9560 Z= 0.176 Angle : 0.725 11.412 12955 Z= 0.374 Chirality : 0.049 0.216 1410 Planarity : 0.006 0.061 1640 Dihedral : 4.997 19.314 1270 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.20 % Allowed : 16.98 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.24), residues: 1120 helix: -0.64 (0.30), residues: 265 sheet: -2.60 (0.25), residues: 330 loop : -2.24 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 169 TYR 0.023 0.002 TYR A 132 PHE 0.019 0.002 PHE A 200 TRP 0.024 0.001 TRP D 53 HIS 0.005 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9560) covalent geometry : angle 0.72492 (12955) hydrogen bonds : bond 0.05143 ( 294) hydrogen bonds : angle 6.12560 ( 903) *********************** 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 193 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7409 (p90) cc_final: 0.6621 (p90) REVERT: A 129 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: B 55 TYR cc_start: 0.7423 (p90) cc_final: 0.6669 (p90) REVERT: B 126 TYR cc_start: 0.5689 (m-80) cc_final: 0.5446 (m-80) REVERT: B 338 MET cc_start: 0.5553 (tpp) cc_final: 0.4944 (tpt) REVERT: C 52 GLN cc_start: 0.7469 (mp10) cc_final: 0.6936 (tt0) REVERT: C 55 TYR cc_start: 0.7526 (p90) cc_final: 0.6665 (p90) REVERT: C 69 GLU cc_start: 0.6376 (tp30) cc_final: 0.6174 (tp30) REVERT: D 55 TYR cc_start: 0.7305 (p90) cc_final: 0.6428 (p90) REVERT: D 257 MET cc_start: 0.5468 (tpt) cc_final: 0.4858 (mmm) REVERT: E 55 TYR cc_start: 0.7303 (p90) cc_final: 0.6362 (p90) REVERT: E 339 ASP cc_start: 0.6624 (t0) cc_final: 0.6380 (p0) outliers start: 43 outliers final: 32 residues processed: 180 average time/residue: 0.0664 time to fit residues: 18.1426 Evaluate side-chains 178 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 75 GLN 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 224 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 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 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 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 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 Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 336 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 8.9990 chunk 90 optimal weight: 0.2980 chunk 112 optimal weight: 0.0970 chunk 64 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.0670 chunk 27 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 55 optimal weight: 0.0970 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN E 9 ASN E 87 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5076 r_free = 0.5076 target = 0.219845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.162805 restraints weight = 9184.212| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 4.03 r_work: 0.4226 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.2978 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= 0.125 Angle : 0.654 10.926 12955 Z= 0.336 Chirality : 0.046 0.224 1410 Planarity : 0.006 0.059 1640 Dihedral : 4.354 17.042 1270 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 3.02 % Allowed : 18.34 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.24), residues: 1120 helix: 0.02 (0.30), residues: 265 sheet: -2.42 (0.24), residues: 351 loop : -1.91 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 218 TYR 0.020 0.001 TYR E 176 PHE 0.016 0.001 PHE C 200 TRP 0.019 0.001 TRP D 53 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9560) covalent geometry : angle 0.65364 (12955) hydrogen bonds : bond 0.04453 ( 294) hydrogen bonds : angle 5.65066 ( 903) *********************** 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 181 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7291 (p90) cc_final: 0.6577 (p90) REVERT: A 75 GLN cc_start: 0.6225 (pm20) cc_final: 0.5654 (mp10) REVERT: A 129 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: B 55 TYR cc_start: 0.7216 (p90) cc_final: 0.6560 (p90) REVERT: B 126 TYR cc_start: 0.5687 (m-80) cc_final: 0.5418 (m-80) REVERT: B 199 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: B 338 MET cc_start: 0.5661 (tpp) cc_final: 0.5032 (tpt) REVERT: C 52 GLN cc_start: 0.7294 (mp10) cc_final: 0.6924 (tt0) REVERT: C 55 TYR cc_start: 0.7392 (p90) cc_final: 0.6614 (p90) REVERT: C 129 GLU cc_start: 0.7052 (mp0) cc_final: 0.6790 (mm-30) REVERT: C 201 GLN cc_start: 0.6983 (mm-40) cc_final: 0.6601 (mm110) REVERT: D 55 TYR cc_start: 0.7164 (p90) cc_final: 0.6385 (p90) REVERT: D 197 GLN cc_start: 0.7335 (pp30) cc_final: 0.7060 (pp30) REVERT: D 257 MET cc_start: 0.5400 (tpt) cc_final: 0.4899 (mmm) outliers start: 31 outliers final: 17 residues processed: 169 average time/residue: 0.0782 time to fit residues: 19.7150 Evaluate side-chains 160 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 230 VAL 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 39 THR Chi-restraints excluded: chain E residue 53 TRP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 TRP Chi-restraints excluded: chain E residue 172 VAL 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 97 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN E 9 ASN 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 = 0.215810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.156893 restraints weight = 9332.173| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 3.51 r_work: 0.4147 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9560 Z= 0.142 Angle : 0.689 11.422 12955 Z= 0.351 Chirality : 0.047 0.228 1410 Planarity : 0.006 0.066 1640 Dihedral : 4.447 17.215 1270 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.05 % Favored : 92.86 % Rotamer: Outliers : 2.24 % Allowed : 20.10 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.24), residues: 1120 helix: -0.07 (0.30), residues: 264 sheet: -2.44 (0.25), residues: 350 loop : -1.98 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 169 TYR 0.014 0.002 TYR E 73 PHE 0.016 0.001 PHE A 200 TRP 0.021 0.001 TRP D 53 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9560) covalent geometry : angle 0.68924 (12955) hydrogen bonds : bond 0.04511 ( 294) hydrogen bonds : angle 5.73312 ( 903) *********************** 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 172 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7392 (p90) cc_final: 0.6541 (p90) REVERT: A 129 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: A 197 GLN cc_start: 0.7595 (mp10) cc_final: 0.7076 (mp10) REVERT: B 55 TYR cc_start: 0.7333 (p90) cc_final: 0.6635 (p90) REVERT: B 126 TYR cc_start: 0.5639 (m-80) cc_final: 0.5343 (m-80) REVERT: B 199 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7354 (pp20) REVERT: B 338 MET cc_start: 0.5556 (tpp) cc_final: 0.4983 (tpt) REVERT: C 52 GLN cc_start: 0.7455 (mp10) cc_final: 0.6943 (tt0) REVERT: C 55 TYR cc_start: 0.7475 (p90) cc_final: 0.6668 (p90) REVERT: C 199 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7105 (tt0) REVERT: C 201 GLN cc_start: 0.7178 (mm110) cc_final: 0.6963 (mm-40) REVERT: D 55 TYR cc_start: 0.7238 (p90) cc_final: 0.6413 (p90) REVERT: D 197 GLN cc_start: 0.7426 (pp30) cc_final: 0.7119 (pp30) REVERT: D 257 MET cc_start: 0.5512 (tpt) cc_final: 0.4931 (mmm) REVERT: E 197 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6630 (pm20) outliers start: 23 outliers final: 17 residues processed: 162 average time/residue: 0.0753 time to fit residues: 18.5652 Evaluate side-chains 163 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN 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 53 TRP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 230 VAL 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 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 104 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN E 9 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.211653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.153765 restraints weight = 9312.551| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 3.36 r_work: 0.4145 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9560 Z= 0.166 Angle : 0.724 11.153 12955 Z= 0.374 Chirality : 0.049 0.219 1410 Planarity : 0.006 0.078 1640 Dihedral : 4.655 17.237 1270 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 2.63 % Allowed : 19.61 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.24), residues: 1120 helix: -0.28 (0.30), residues: 264 sheet: -2.50 (0.25), residues: 351 loop : -2.06 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 169 TYR 0.021 0.002 TYR A 132 PHE 0.017 0.002 PHE A 200 TRP 0.023 0.001 TRP D 53 HIS 0.004 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9560) covalent geometry : angle 0.72379 (12955) hydrogen bonds : bond 0.04778 ( 294) hydrogen bonds : angle 5.88713 ( 903) ********************** 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 168 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.7377 (p90) cc_final: 0.6608 (p90) REVERT: A 129 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 55 TYR cc_start: 0.7380 (p90) cc_final: 0.6674 (p90) REVERT: B 126 TYR cc_start: 0.5667 (m-80) cc_final: 0.5393 (m-80) REVERT: B 199 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7381 (pp20) REVERT: B 338 MET cc_start: 0.5535 (tpp) cc_final: 0.4936 (tpt) REVERT: C 52 GLN cc_start: 0.7502 (mp10) cc_final: 0.6995 (tt0) REVERT: C 55 TYR cc_start: 0.7478 (p90) cc_final: 0.6678 (p90) REVERT: C 199 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7313 (tm-30) REVERT: D 55 TYR cc_start: 0.7239 (p90) cc_final: 0.6414 (p90) REVERT: D 197 GLN cc_start: 0.7528 (pp30) cc_final: 0.7267 (pp30) REVERT: D 257 MET cc_start: 0.5485 (tpt) cc_final: 0.4892 (mmm) REVERT: E 197 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6754 (pm20) outliers start: 27 outliers final: 19 residues processed: 159 average time/residue: 0.0676 time to fit residues: 16.3784 Evaluate side-chains 163 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN 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 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 206 VAL Chi-restraints excluded: chain C residue 230 VAL 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 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 63 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 0.0030 chunk 84 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.212666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.154518 restraints weight = 9283.970| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.40 r_work: 0.4132 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9560 Z= 0.164 Angle : 0.981 59.195 12955 Z= 0.550 Chirality : 0.048 0.201 1410 Planarity : 0.006 0.080 1640 Dihedral : 4.641 17.024 1270 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 2.54 % Allowed : 19.90 % Favored : 77.56 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.24), residues: 1120 helix: -0.28 (0.30), residues: 264 sheet: -2.50 (0.25), residues: 351 loop : -2.06 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 169 TYR 0.020 0.002 TYR A 132 PHE 0.017 0.002 PHE A 200 TRP 0.022 0.001 TRP D 53 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9560) covalent geometry : angle 0.98141 (12955) hydrogen bonds : bond 0.04688 ( 294) hydrogen bonds : angle 5.88715 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2834.68 seconds wall clock time: 49 minutes 18.28 seconds (2958.28 seconds total)