Starting phenix.real_space_refine on Fri Aug 7 09:05:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9do8_47074/08_2026/9do8_47074_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9do8_47074/08_2026/9do8_47074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9do8_47074/08_2026/9do8_47074_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9do8_47074/08_2026/9do8_47074_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9do8_47074/08_2026/9do8_47074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9do8_47074/08_2026/9do8_47074.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians S 24 5.16 5 C 6295 2.51 5 N 1723 2.21 5 O 1941 1.98 5 H 9847 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19830 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2046 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "B" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2046 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "C" Number of atoms: 5831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 5831 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 346} Chain breaks: 4 Chain: "D" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2046 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "E" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2046 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain: "F" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 5815 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 345} Chain breaks: 4 Time building chain proxies: 2.88, per 1000 atoms: 0.15 Number of scatterers: 19830 At special positions: 0 Unit cell: (110.39, 94.62, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 1941 8.00 N 1723 7.00 C 6295 6.00 H 9847 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 538.3 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 21 sheets defined 16.4% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 189 through 201 Processing helix chain 'C' and resid 204 through 220 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 304 through 312 Processing helix chain 'C' and resid 313 through 318 removed outlier: 6.348A pdb=" N GLU C 316 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 444 through 447 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 80 through 83 removed outlier: 4.231A pdb=" N GLY D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 83' Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'F' and resid 54 through 60 Processing helix chain 'F' and resid 61 through 72 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 189 through 201 Processing helix chain 'F' and resid 204 through 220 Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.504A pdb=" N ILE F 302 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 311 Processing helix chain 'F' and resid 312 through 318 removed outlier: 5.775A pdb=" N SER F 315 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU F 316 " --> pdb=" O ASN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 334 through 345 removed outlier: 3.660A pdb=" N GLN F 340 " --> pdb=" O PRO F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 447 removed outlier: 3.525A pdb=" N THR F 447 " --> pdb=" O PRO F 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 444 through 447' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.088A pdb=" N LEU A 31 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN A 60 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP A 6 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE A 129 " --> pdb=" O TRP A 6 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE A 8 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL A 131 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE A 10 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR A 133 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS A 12 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.615A pdb=" N VAL A 19 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS A 22 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 78 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 24 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASP A 76 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA A 26 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 74 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR A 71 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP A 93 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 73 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR A 91 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 75 " --> pdb=" O HIS A 89 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N HIS A 89 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 77 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 41 removed outlier: 6.368A pdb=" N ALA B 39 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU B 31 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN B 60 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE B 129 " --> pdb=" O TRP B 6 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE B 8 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 131 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B 10 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 133 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS B 12 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.896A pdb=" N THR B 71 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 93 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 73 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR B 91 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 75 " --> pdb=" O HIS B 89 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N HIS B 89 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 77 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 76 through 79 removed outlier: 5.198A pdb=" N GLY C 77 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 103 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 100 through 103 current: chain 'C' and resid 162 through 174 removed outlier: 5.983A pdb=" N SER C 163 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR C 237 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG C 165 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA C 235 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU C 167 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU C 233 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY C 231 " --> pdb=" O PRO C 169 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 171 " --> pdb=" O ILE C 229 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 291 through 295 current: chain 'F' and resid 161 through 174 removed outlier: 6.547A pdb=" N ILE F 229 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG F 172 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL F 227 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP F 174 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N THR F 225 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 380 through 381 Processing sheet with id=AA8, first strand: chain 'C' and resid 355 through 357 Processing sheet with id=AA9, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AB1, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AB2, first strand: chain 'C' and resid 460 through 464 removed outlier: 3.689A pdb=" N SER C 492 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 32 removed outlier: 4.505A pdb=" N ASN D 60 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TRP D 6 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 129 " --> pdb=" O TRP D 6 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 8 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL D 131 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE D 10 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR D 133 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS D 12 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.554A pdb=" N VAL D 19 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU D 24 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR D 74 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA D 26 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR D 72 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR D 71 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP D 93 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY D 73 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR D 91 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE D 75 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N HIS D 89 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU D 77 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 40 through 41 removed outlier: 4.116A pdb=" N LEU E 31 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN E 60 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP E 6 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE E 129 " --> pdb=" O TRP E 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE E 8 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 131 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE E 10 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR E 133 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS E 12 " --> pdb=" O THR E 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 50 through 51 removed outlier: 4.410A pdb=" N LEU E 24 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR E 74 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA E 26 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR E 72 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR E 71 " --> pdb=" O ASP E 93 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP E 93 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY E 73 " --> pdb=" O TYR E 91 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR E 91 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE E 75 " --> pdb=" O HIS E 89 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS E 89 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU E 77 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 79 removed outlier: 5.067A pdb=" N GLY F 77 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 380 through 381 Processing sheet with id=AB9, first strand: chain 'F' and resid 355 through 357 Processing sheet with id=AC1, first strand: chain 'F' and resid 421 through 423 Processing sheet with id=AC2, first strand: chain 'F' and resid 456 through 458 Processing sheet with id=AC3, first strand: chain 'F' and resid 460 through 464 removed outlier: 3.862A pdb=" N SER F 492 " --> pdb=" O THR F 475 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 789 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: 3.87 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9841 1.02 - 1.22: 21 1.22 - 1.42: 4167 1.42 - 1.62: 5975 1.62 - 1.82: 42 Bond restraints: 20046 Sorted by residual: bond pdb=" CA LYS D 135 " pdb=" C LYS D 135 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.27e-02 6.20e+03 2.44e+01 bond pdb=" CA LYS A 135 " pdb=" C LYS A 135 " ideal model delta sigma weight residual 1.526 1.470 0.056 1.30e-02 5.92e+03 1.83e+01 bond pdb=" CA ALA A 67 " pdb=" C ALA A 67 " ideal model delta sigma weight residual 1.521 1.477 0.044 1.21e-02 6.83e+03 1.33e+01 bond pdb=" NZ LYS B 135 " pdb=" HZ3 LYS B 135 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" NZ LYS B 136 " pdb=" HZ2 LYS B 136 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 20041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 32346 1.60 - 3.21: 3562 3.21 - 4.81: 312 4.81 - 6.42: 64 6.42 - 8.02: 6 Bond angle restraints: 36290 Sorted by residual: angle pdb=" N LYS B 135 " pdb=" CA LYS B 135 " pdb=" C LYS B 135 " ideal model delta sigma weight residual 113.18 119.62 -6.44 1.21e+00 6.83e-01 2.84e+01 angle pdb=" N ALA E 26 " pdb=" CA ALA E 26 " pdb=" C ALA E 26 " ideal model delta sigma weight residual 108.90 116.92 -8.02 1.63e+00 3.76e-01 2.42e+01 angle pdb=" N GLY F 521 " pdb=" CA GLY F 521 " pdb=" C GLY F 521 " ideal model delta sigma weight residual 115.32 108.94 6.38 1.38e+00 5.25e-01 2.13e+01 angle pdb=" N PHE D 90 " pdb=" CA PHE D 90 " pdb=" C PHE D 90 " ideal model delta sigma weight residual 109.50 115.94 -6.44 1.58e+00 4.01e-01 1.66e+01 angle pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 111.45 107.79 3.66 9.30e-01 1.16e+00 1.55e+01 ... (remaining 36285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8655 17.72 - 35.44: 496 35.44 - 53.17: 212 53.17 - 70.89: 51 70.89 - 88.61: 9 Dihedral angle restraints: 9423 sinusoidal: 5168 harmonic: 4255 Sorted by residual: dihedral pdb=" CA ARG B 64 " pdb=" C ARG B 64 " pdb=" N SER B 65 " pdb=" CA SER B 65 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR F 461 " pdb=" C TYR F 461 " pdb=" N GLU F 462 " pdb=" CA GLU F 462 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TYR F 473 " pdb=" C TYR F 473 " pdb=" N VAL F 474 " pdb=" CA VAL F 474 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 9420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1142 0.040 - 0.081: 236 0.081 - 0.121: 142 0.121 - 0.161: 29 0.161 - 0.201: 1 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA LYS B 135 " pdb=" N LYS B 135 " pdb=" C LYS B 135 " pdb=" CB LYS B 135 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE E 59 " pdb=" N ILE E 59 " pdb=" C ILE E 59 " pdb=" CB ILE E 59 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ASP C 174 " pdb=" N ASP C 174 " pdb=" C ASP C 174 " pdb=" CB ASP C 174 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1547 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 413 " -0.032 2.00e-02 2.50e+03 3.24e-02 1.57e+01 pdb=" CD GLN F 413 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN F 413 " 0.027 2.00e-02 2.50e+03 pdb=" NE2 GLN F 413 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN F 413 " 0.046 2.00e-02 2.50e+03 pdb="HE22 GLN F 413 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 112 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C THR F 112 " 0.040 2.00e-02 2.50e+03 pdb=" O THR F 112 " -0.015 2.00e-02 2.50e+03 pdb=" N THR F 113 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 478 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C VAL F 478 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL F 478 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP F 479 " 0.012 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1409 2.22 - 2.81: 42373 2.81 - 3.41: 52692 3.41 - 4.00: 73566 4.00 - 4.60: 110210 Nonbonded interactions: 280250 Sorted by model distance: nonbonded pdb=" O ASN A 13 " pdb=" H ASP A 54 " model vdw 1.620 2.450 nonbonded pdb=" O ASP C 384 " pdb=" HG SER C 432 " model vdw 1.624 2.450 nonbonded pdb=" HH TYR F 461 " pdb=" O PRO F 507 " model vdw 1.628 2.450 nonbonded pdb=" O TYR D 3 " pdb=" HZ3 LYS D 37 " model vdw 1.634 2.450 nonbonded pdb="HD22 ASN C 304 " pdb=" OE2 GLU C 307 " model vdw 1.666 2.450 ... (remaining 280245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 52 through 479 or resid 484 through 522)) selection = chain 'F' } 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: 8.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.390 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:5.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 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 : 0.004 0.063 10199 Z= 0.250 Angle : 0.620 8.020 13850 Z= 0.368 Chirality : 0.046 0.201 1550 Planarity : 0.004 0.045 1781 Dihedral : 11.641 88.611 3722 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.32 (0.23), residues: 1261 helix: 1.30 (0.47), residues: 139 sheet: -0.28 (0.25), residues: 424 loop : 0.49 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 404 TYR 0.022 0.001 TYR C 161 PHE 0.008 0.001 PHE A 75 TRP 0.007 0.001 TRP D 96 HIS 0.007 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.25 (10199) covalent geometry : angle 0.62040 / 0.37 (13850) hydrogen bonds : bond 0.15540 / 10.70 ( 312) hydrogen bonds : angle 6.42598 / 4.39 ( 789) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7328 (m-30) cc_final: 0.6921 (m-30) REVERT: A 102 THR cc_start: 0.6907 (m) cc_final: 0.6476 (p) REVERT: B 51 VAL cc_start: 0.6470 (t) cc_final: 0.6186 (m) REVERT: B 57 LEU cc_start: 0.7547 (tp) cc_final: 0.7344 (tm) REVERT: B 101 ASN cc_start: 0.7510 (m-40) cc_final: 0.7098 (m-40) REVERT: B 119 GLN cc_start: 0.7241 (pm20) cc_final: 0.6951 (pm20) REVERT: B 121 LEU cc_start: 0.7044 (mt) cc_final: 0.6693 (mm) REVERT: C 60 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8034 (mm-40) REVERT: C 71 ASP cc_start: 0.8115 (m-30) cc_final: 0.7888 (m-30) REVERT: C 165 ARG cc_start: 0.7520 (ttt-90) cc_final: 0.7294 (ttt-90) REVERT: C 186 ILE cc_start: 0.7856 (pt) cc_final: 0.7539 (pp) REVERT: C 187 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8114 (mtmt) REVERT: C 197 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7734 (mp10) REVERT: C 354 ASP cc_start: 0.7784 (p0) cc_final: 0.7417 (p0) REVERT: C 372 LYS cc_start: 0.7526 (ttpp) cc_final: 0.7176 (ttpp) REVERT: C 425 LEU cc_start: 0.7816 (mm) cc_final: 0.7557 (mt) REVERT: C 491 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7783 (mtmm) REVERT: D 23 ASN cc_start: 0.7721 (m-40) cc_final: 0.7207 (m-40) REVERT: D 76 ASP cc_start: 0.6416 (m-30) cc_final: 0.5858 (m-30) REVERT: D 93 ASP cc_start: 0.5994 (t0) cc_final: 0.5638 (t0) REVERT: D 126 LEU cc_start: 0.6680 (tp) cc_final: 0.6473 (tp) REVERT: D 134 LEU cc_start: 0.7246 (tp) cc_final: 0.7025 (tp) REVERT: E 17 GLN cc_start: 0.6382 (mp10) cc_final: 0.6151 (mp10) REVERT: E 101 ASN cc_start: 0.7069 (m-40) cc_final: 0.6564 (m-40) REVERT: F 110 GLU cc_start: 0.8146 (tt0) cc_final: 0.7866 (tp30) REVERT: F 210 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7222 (mm-30) REVERT: F 304 ASN cc_start: 0.8149 (t0) cc_final: 0.7907 (t0) REVERT: F 463 MET cc_start: 0.7507 (ttm) cc_final: 0.7300 (ttt) REVERT: F 464 HIS cc_start: 0.7328 (m90) cc_final: 0.7058 (m170) REVERT: F 491 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7834 (mtpp) REVERT: F 515 MET cc_start: 0.8278 (mmp) cc_final: 0.7750 (mmt) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.8166 time to fit residues: 293.3862 Evaluate side-chains 299 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.0060 chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 45 ASN F 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.121108 restraints weight = 42591.252| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.10 r_work: 0.3500 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10199 Z= 0.127 Angle : 0.500 4.270 13850 Z= 0.263 Chirality : 0.045 0.160 1550 Planarity : 0.004 0.028 1781 Dihedral : 4.586 18.769 1361 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.28 % Allowed : 9.61 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.34 (0.23), residues: 1261 helix: 1.28 (0.45), residues: 142 sheet: 0.00 (0.25), residues: 396 loop : 0.28 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 452 TYR 0.014 0.001 TYR D 46 PHE 0.010 0.001 PHE E 90 TRP 0.009 0.001 TRP E 92 HIS 0.010 0.001 HIS C 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10199) covalent geometry : angle 0.49990 / 0.26 (13850) hydrogen bonds : bond 0.03577 / 2.41 ( 312) hydrogen bonds : angle 5.30696 / 3.62 ( 789) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 307 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7598 (ttpp) cc_final: 0.7289 (ttpp) REVERT: A 102 THR cc_start: 0.8161 (m) cc_final: 0.7938 (p) REVERT: B 119 GLN cc_start: 0.8206 (pm20) cc_final: 0.7913 (pm20) REVERT: C 186 ILE cc_start: 0.7967 (pt) cc_final: 0.7718 (pp) REVERT: C 187 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8308 (mtmt) REVERT: C 197 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7839 (mp10) REVERT: C 210 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7510 (mm-30) REVERT: C 218 GLU cc_start: 0.6658 (pt0) cc_final: 0.6391 (pt0) REVERT: C 307 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7574 (mt-10) REVERT: C 372 LYS cc_start: 0.8006 (ttpp) cc_final: 0.7707 (ttpp) REVERT: F 210 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7656 (mm-30) REVERT: F 515 MET cc_start: 0.8632 (mmp) cc_final: 0.7977 (mmt) outliers start: 14 outliers final: 8 residues processed: 309 average time/residue: 0.8427 time to fit residues: 289.2069 Evaluate side-chains 311 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 303 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 54 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.2451 > 50:) overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 295 ASN F 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117078 restraints weight = 43768.892| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.09 r_work: 0.3443 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 10199 Z= 0.250 Angle : 0.560 4.652 13850 Z= 0.297 Chirality : 0.047 0.155 1550 Planarity : 0.004 0.037 1781 Dihedral : 5.022 19.259 1361 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.10 % Allowed : 12.35 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.05 (0.22), residues: 1261 helix: 1.02 (0.44), residues: 142 sheet: 0.11 (0.26), residues: 357 loop : -0.11 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 449 TYR 0.012 0.002 TYR F 430 PHE 0.014 0.002 PHE A 90 TRP 0.016 0.002 TRP E 92 HIS 0.014 0.002 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 (10199) covalent geometry : angle 0.56004 / 0.30 (13850) hydrogen bonds : bond 0.03962 / 2.76 ( 312) hydrogen bonds : angle 5.37099 / 3.67 ( 789) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 317 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7717 (ttpp) cc_final: 0.7409 (ttpp) REVERT: C 187 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8330 (mtmt) REVERT: C 197 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7916 (mp10) REVERT: C 370 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7909 (mtt180) REVERT: E 135 LYS cc_start: 0.7184 (tppt) cc_final: 0.6915 (mttt) REVERT: F 57 ASP cc_start: 0.8082 (m-30) cc_final: 0.7874 (m-30) REVERT: F 210 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7663 (mm-30) REVERT: F 226 LYS cc_start: 0.8549 (mttt) cc_final: 0.8306 (mttp) outliers start: 23 outliers final: 13 residues processed: 322 average time/residue: 0.8509 time to fit residues: 304.4062 Evaluate side-chains 324 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 311 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 0.0980 chunk 121 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 340 GLN E 45 ASN F 295 ASN F 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.118883 restraints weight = 42685.923| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.11 r_work: 0.3469 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10199 Z= 0.196 Angle : 0.526 4.489 13850 Z= 0.277 Chirality : 0.045 0.151 1550 Planarity : 0.004 0.035 1781 Dihedral : 4.895 19.099 1361 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.47 % Allowed : 13.45 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.01 (0.22), residues: 1261 helix: 1.06 (0.44), residues: 142 sheet: 0.10 (0.26), residues: 357 loop : -0.17 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 64 TYR 0.017 0.002 TYR A 3 PHE 0.010 0.002 PHE A 75 TRP 0.013 0.001 TRP E 92 HIS 0.009 0.002 HIS D 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (10199) covalent geometry : angle 0.52614 / 0.28 (13850) hydrogen bonds : bond 0.03460 / 2.39 ( 312) hydrogen bonds : angle 5.23599 / 3.58 ( 789) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 321 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7750 (ttpp) cc_final: 0.7440 (ttpp) REVERT: C 187 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8332 (mtmt) REVERT: C 197 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7816 (mp10) REVERT: C 226 LYS cc_start: 0.8720 (mttt) cc_final: 0.8455 (mttp) REVERT: C 413 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6660 (mm-40) REVERT: E 135 LYS cc_start: 0.7159 (tppt) cc_final: 0.6897 (mttt) REVERT: F 210 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7652 (mm-30) REVERT: F 218 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7601 (mm-30) REVERT: F 362 GLU cc_start: 0.7841 (mp0) cc_final: 0.7592 (mp0) REVERT: F 515 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7935 (mmt) outliers start: 27 outliers final: 15 residues processed: 325 average time/residue: 0.8019 time to fit residues: 289.4945 Evaluate side-chains 334 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 317 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 427 GLN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 515 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 118 optimal weight: 0.0060 chunk 94 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 340 GLN F 295 ASN F 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119179 restraints weight = 42310.793| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.09 r_work: 0.3464 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 10199 Z= 0.226 Angle : 0.542 4.442 13850 Z= 0.287 Chirality : 0.046 0.159 1550 Planarity : 0.004 0.037 1781 Dihedral : 4.979 19.634 1361 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.47 % Allowed : 15.00 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.14 (0.22), residues: 1261 helix: 1.01 (0.43), residues: 142 sheet: -0.02 (0.26), residues: 361 loop : -0.27 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 64 TYR 0.019 0.002 TYR A 3 PHE 0.011 0.002 PHE F 488 TRP 0.015 0.002 TRP E 92 HIS 0.009 0.002 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (10199) covalent geometry : angle 0.54189 / 0.29 (13850) hydrogen bonds : bond 0.03564 / 2.47 ( 312) hydrogen bonds : angle 5.29026 / 3.62 ( 789) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 318 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7776 (ttpp) cc_final: 0.7480 (ttpp) REVERT: B 121 LEU cc_start: 0.8269 (mm) cc_final: 0.8008 (mt) REVERT: C 187 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8340 (mtmt) REVERT: C 413 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6657 (mm-40) REVERT: F 110 GLU cc_start: 0.5290 (mm-30) cc_final: 0.4234 (mm-30) REVERT: F 210 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7624 (mm-30) REVERT: F 288 LEU cc_start: 0.7318 (tt) cc_final: 0.7102 (tm) outliers start: 27 outliers final: 19 residues processed: 322 average time/residue: 0.7792 time to fit residues: 278.8933 Evaluate side-chains 338 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 318 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 519 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 54 optimal weight: 0.0870 chunk 55 optimal weight: 0.0000 chunk 11 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 340 GLN F 295 ASN F 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119758 restraints weight = 42307.305| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.11 r_work: 0.3477 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10199 Z= 0.131 Angle : 0.501 4.419 13850 Z= 0.262 Chirality : 0.044 0.148 1550 Planarity : 0.004 0.036 1781 Dihedral : 4.671 18.782 1361 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.10 % Allowed : 15.92 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: 0.03 (0.22), residues: 1261 helix: 1.23 (0.44), residues: 142 sheet: 0.11 (0.27), residues: 357 loop : -0.19 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 64 TYR 0.014 0.001 TYR A 3 PHE 0.008 0.001 PHE F 488 TRP 0.010 0.001 TRP B 92 HIS 0.006 0.001 HIS D 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (10199) covalent geometry : angle 0.50084 / 0.26 (13850) hydrogen bonds : bond 0.03115 / 2.14 ( 312) hydrogen bonds : angle 5.05856 / 3.46 ( 789) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 316 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7471 (ttpp) REVERT: B 121 LEU cc_start: 0.8279 (mm) cc_final: 0.8020 (mt) REVERT: C 97 ASP cc_start: 0.8110 (m-30) cc_final: 0.7877 (m-30) REVERT: C 187 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8306 (mtmt) REVERT: C 413 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6631 (mm-40) REVERT: D 52 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7887 (mtmm) REVERT: F 110 GLU cc_start: 0.5430 (mm-30) cc_final: 0.4334 (mm-30) REVERT: F 210 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7598 (mm-30) REVERT: F 288 LEU cc_start: 0.7303 (tt) cc_final: 0.7087 (tm) outliers start: 23 outliers final: 13 residues processed: 320 average time/residue: 0.8226 time to fit residues: 292.5034 Evaluate side-chains 327 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 313 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 120 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 340 GLN F 295 ASN F 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116935 restraints weight = 43610.711| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.08 r_work: 0.3453 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 10199 Z= 0.230 Angle : 0.550 4.556 13850 Z= 0.291 Chirality : 0.046 0.167 1550 Planarity : 0.004 0.037 1781 Dihedral : 4.916 19.453 1361 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.93 % Allowed : 15.37 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.16 (0.22), residues: 1261 helix: 1.04 (0.43), residues: 142 sheet: -0.17 (0.27), residues: 363 loop : -0.23 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 64 TYR 0.018 0.002 TYR A 3 PHE 0.012 0.002 PHE F 488 TRP 0.016 0.002 TRP E 92 HIS 0.011 0.002 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 (10199) covalent geometry : angle 0.55012 / 0.29 (13850) hydrogen bonds : bond 0.03498 / 2.43 ( 312) hydrogen bonds : angle 5.25662 / 3.59 ( 789) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 323 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7743 (ttpp) cc_final: 0.7442 (ttpp) REVERT: B 121 LEU cc_start: 0.8273 (mm) cc_final: 0.8008 (mt) REVERT: C 97 ASP cc_start: 0.8129 (m-30) cc_final: 0.7779 (m-30) REVERT: C 187 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8317 (mtmt) REVERT: C 197 GLN cc_start: 0.8039 (mp10) cc_final: 0.7628 (mp10) REVERT: C 413 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6607 (mm-40) REVERT: D 52 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7875 (mtmm) REVERT: F 110 GLU cc_start: 0.5595 (mm-30) cc_final: 0.4138 (mm-30) REVERT: F 210 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7640 (mm-30) REVERT: F 288 LEU cc_start: 0.7365 (tt) cc_final: 0.7110 (tm) outliers start: 32 outliers final: 19 residues processed: 329 average time/residue: 0.7724 time to fit residues: 282.0344 Evaluate side-chains 339 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 319 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 519 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 85 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 340 GLN C 440 HIS F 295 ASN F 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118014 restraints weight = 43485.220| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.09 r_work: 0.3466 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10199 Z= 0.148 Angle : 0.515 4.505 13850 Z= 0.271 Chirality : 0.044 0.152 1550 Planarity : 0.004 0.035 1781 Dihedral : 4.698 18.703 1361 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.20 % Allowed : 16.56 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.07 (0.23), residues: 1261 helix: 1.19 (0.43), residues: 142 sheet: -0.13 (0.27), residues: 363 loop : -0.16 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 106 TYR 0.013 0.001 TYR A 3 PHE 0.011 0.001 PHE C 435 TRP 0.011 0.001 TRP C 381 HIS 0.006 0.001 HIS C 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10199) covalent geometry : angle 0.51539 / 0.27 (13850) hydrogen bonds : bond 0.03143 / 2.17 ( 312) hydrogen bonds : angle 5.09937 / 3.49 ( 789) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 320 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7759 (ttpp) cc_final: 0.7463 (ttpp) REVERT: B 121 LEU cc_start: 0.8284 (mm) cc_final: 0.8008 (mt) REVERT: C 97 ASP cc_start: 0.8132 (m-30) cc_final: 0.7780 (m-30) REVERT: C 187 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8314 (mtmt) REVERT: C 197 GLN cc_start: 0.8009 (mp10) cc_final: 0.7592 (mp10) REVERT: C 413 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6593 (mm-40) REVERT: D 52 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7911 (mtmm) REVERT: F 110 GLU cc_start: 0.5547 (mm-30) cc_final: 0.4121 (mm-30) REVERT: F 210 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7594 (mm-30) REVERT: F 288 LEU cc_start: 0.7329 (tt) cc_final: 0.7092 (tm) outliers start: 24 outliers final: 15 residues processed: 326 average time/residue: 0.7406 time to fit residues: 268.9883 Evaluate side-chains 332 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 316 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.0060 chunk 91 optimal weight: 0.2980 chunk 106 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 340 GLN C 440 HIS E 45 ASN F 295 ASN F 405 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.118420 restraints weight = 43346.526| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.06 r_work: 0.3468 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 10199 Z= 0.163 Angle : 0.522 4.588 13850 Z= 0.274 Chirality : 0.045 0.154 1550 Planarity : 0.004 0.034 1781 Dihedral : 4.687 18.488 1361 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.29 % Allowed : 16.65 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.06 (0.23), residues: 1261 helix: 1.22 (0.43), residues: 142 sheet: -0.12 (0.27), residues: 363 loop : -0.17 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 88 TYR 0.013 0.001 TYR A 3 PHE 0.010 0.001 PHE C 435 TRP 0.012 0.001 TRP C 381 HIS 0.007 0.002 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (10199) covalent geometry : angle 0.52164 / 0.27 (13850) hydrogen bonds : bond 0.03177 / 2.20 ( 312) hydrogen bonds : angle 5.08237 / 3.48 ( 789) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 315 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7448 (ttpp) REVERT: B 121 LEU cc_start: 0.8270 (mm) cc_final: 0.8016 (mt) REVERT: C 97 ASP cc_start: 0.8129 (m-30) cc_final: 0.7782 (m-30) REVERT: C 187 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8304 (mtmt) REVERT: C 197 GLN cc_start: 0.8006 (mp10) cc_final: 0.7589 (mp10) REVERT: C 340 GLN cc_start: 0.8420 (mt0) cc_final: 0.8130 (mt0) REVERT: C 413 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6594 (mm-40) REVERT: D 52 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7911 (mtmm) REVERT: F 110 GLU cc_start: 0.5735 (mm-30) cc_final: 0.3787 (mm-30) REVERT: F 210 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7602 (mm-30) REVERT: F 288 LEU cc_start: 0.7364 (tt) cc_final: 0.7126 (tm) outliers start: 25 outliers final: 17 residues processed: 320 average time/residue: 0.7846 time to fit residues: 279.1941 Evaluate side-chains 331 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 313 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 62 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 440 HIS E 45 ASN F 295 ASN F 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116308 restraints weight = 43437.786| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.08 r_work: 0.3452 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10199 Z= 0.218 Angle : 0.556 4.954 13850 Z= 0.294 Chirality : 0.046 0.164 1550 Planarity : 0.004 0.035 1781 Dihedral : 4.874 19.451 1361 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.20 % Allowed : 17.29 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.19 (0.23), residues: 1261 helix: 1.06 (0.43), residues: 142 sheet: -0.16 (0.27), residues: 363 loop : -0.27 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 64 TYR 0.038 0.002 TYR C 473 PHE 0.012 0.002 PHE F 488 TRP 0.015 0.002 TRP E 92 HIS 0.009 0.002 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (10199) covalent geometry : angle 0.55630 / 0.29 (13850) hydrogen bonds : bond 0.03414 / 2.39 ( 312) hydrogen bonds : angle 5.23641 / 3.58 ( 789) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 320 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7765 (ttpp) cc_final: 0.7463 (ttpp) REVERT: A 86 GLN cc_start: 0.7591 (tt0) cc_final: 0.7370 (tt0) REVERT: B 121 LEU cc_start: 0.8280 (mm) cc_final: 0.8040 (mt) REVERT: C 97 ASP cc_start: 0.8141 (m-30) cc_final: 0.7801 (m-30) REVERT: C 187 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8307 (mtmt) REVERT: C 197 GLN cc_start: 0.8021 (mp10) cc_final: 0.7602 (mp10) REVERT: C 413 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6566 (mm-40) REVERT: D 52 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7912 (mtmm) REVERT: F 110 GLU cc_start: 0.5746 (mm-30) cc_final: 0.3773 (mm-30) REVERT: F 210 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7624 (mm-30) REVERT: F 288 LEU cc_start: 0.7364 (tt) cc_final: 0.7108 (tm) REVERT: F 390 LYS cc_start: 0.8459 (pttt) cc_final: 0.8210 (pttm) outliers start: 24 outliers final: 18 residues processed: 327 average time/residue: 0.7976 time to fit residues: 290.3834 Evaluate side-chains 339 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 320 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 64 ARG Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 0.7980 chunk 111 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 118 optimal weight: 0.1980 chunk 98 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 80 optimal weight: 0.0020 overall best weight: 0.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 340 GLN C 440 HIS F 295 ASN F 405 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119222 restraints weight = 43708.486| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.07 r_work: 0.3480 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10199 Z= 0.108 Angle : 0.503 4.540 13850 Z= 0.262 Chirality : 0.044 0.144 1550 Planarity : 0.004 0.046 1781 Dihedral : 4.486 15.947 1361 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.46 % Allowed : 18.12 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.00 (0.23), residues: 1261 helix: 1.36 (0.44), residues: 142 sheet: -0.05 (0.27), residues: 358 loop : -0.16 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 88 TYR 0.030 0.001 TYR C 473 PHE 0.006 0.001 PHE F 488 TRP 0.009 0.001 TRP C 381 HIS 0.006 0.001 HIS C 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (10199) covalent geometry : angle 0.50262 / 0.26 (13850) hydrogen bonds : bond 0.02870 / 1.99 ( 312) hydrogen bonds : angle 4.97131 / 3.40 ( 789) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7838.74 seconds wall clock time: 133 minutes 2.02 seconds (7982.02 seconds total)