Starting phenix.real_space_refine on Tue Jan 13 23:20:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oeu_12864/01_2026/7oeu_12864.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oeu_12864/01_2026/7oeu_12864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oeu_12864/01_2026/7oeu_12864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oeu_12864/01_2026/7oeu_12864.map" model { file = "/net/cci-nas-00/data/ceres_data/7oeu_12864/01_2026/7oeu_12864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oeu_12864/01_2026/7oeu_12864.cif" } resolution = 2.64 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= 0.002 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 25 5.16 5 C 6630 2.51 5 N 1820 2.21 5 O 1990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10465 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2034 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "1" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 59 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Restraints were copied for chains: B, C, D, E, 2, 3, 4, 5 Time building chain proxies: 1.43, per 1000 atoms: 0.14 Number of scatterers: 10465 At special positions: 0 Unit cell: (97.148, 148.004, 134.964, 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 25 16.00 O 1990 8.00 N 1820 7.00 C 6630 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: 0.66 Conformation dependent library (CDL) restraints added in 522.5 milliseconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 40.0% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.863A pdb=" N VAL A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 122 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 162 removed outlier: 4.207A pdb=" N LEU A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 190 through 198 removed outlier: 3.686A pdb=" N VAL A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 12 through 31 Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.863A pdb=" N VAL B 92 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 122 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 147 through 162 removed outlier: 4.207A pdb=" N LEU B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 190 through 198 removed outlier: 3.685A pdb=" N VAL B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 12 through 31 Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.863A pdb=" N VAL C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 162 removed outlier: 4.207A pdb=" N LEU C 153 " --> pdb=" O PRO C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.686A pdb=" N VAL C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 12 through 31 Processing helix chain 'D' and resid 32 through 36 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.862A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 130 through 135 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 147 through 162 removed outlier: 4.208A pdb=" N LEU D 153 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 190 through 198 removed outlier: 3.685A pdb=" N VAL D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 12 through 31 Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.863A pdb=" N VAL E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 94 " --> pdb=" O ASP E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 122 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 147 through 162 removed outlier: 4.207A pdb=" N LEU E 153 " --> pdb=" O PRO E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 Processing helix chain 'E' and resid 190 through 198 removed outlier: 3.686A pdb=" N VAL E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.310A pdb=" N ASP A 38 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL A 226 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A 40 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.310A pdb=" N ASP A 38 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL A 226 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A 40 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 245 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR A 234 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 247 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE A 232 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 57 removed outlier: 7.343A pdb=" N THR A 52 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLN A 73 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU A 54 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.310A pdb=" N ASP B 38 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL B 226 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG B 40 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.310A pdb=" N ASP B 38 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL B 226 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG B 40 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE B 245 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR B 234 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA B 247 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE B 232 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 57 removed outlier: 7.343A pdb=" N THR B 52 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLN B 73 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 54 " --> pdb=" O GLN B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA9, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.309A pdb=" N ASP C 38 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL C 226 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG C 40 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.309A pdb=" N ASP C 38 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL C 226 " --> pdb=" O ASP C 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG C 40 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE C 245 " --> pdb=" O TYR C 234 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR C 234 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA C 247 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE C 232 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 49 through 57 removed outlier: 7.343A pdb=" N THR C 52 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLN C 73 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU C 54 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB4, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.309A pdb=" N ASP D 38 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL D 226 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG D 40 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.309A pdb=" N ASP D 38 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL D 226 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG D 40 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE D 245 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR D 234 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA D 247 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE D 232 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 49 through 57 removed outlier: 7.342A pdb=" N THR D 52 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLN D 73 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU D 54 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 203 through 205 Processing sheet with id=AB8, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.310A pdb=" N ASP E 38 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL E 226 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG E 40 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.310A pdb=" N ASP E 38 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL E 226 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG E 40 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE E 245 " --> pdb=" O TYR E 234 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR E 234 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA E 247 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE E 232 " --> pdb=" O ALA E 247 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 49 through 57 removed outlier: 7.342A pdb=" N THR E 52 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLN E 73 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU E 54 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 203 through 205 490 hydrogen bonds defined for protein. 1350 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: 1.69 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3585 1.34 - 1.46: 2017 1.46 - 1.58: 5028 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 10680 Sorted by residual: bond pdb=" CA ARG E 264 " pdb=" C ARG E 264 " ideal model delta sigma weight residual 1.523 1.538 -0.014 1.34e-02 5.57e+03 1.16e+00 bond pdb=" CA ARG A 264 " pdb=" C ARG A 264 " ideal model delta sigma weight residual 1.523 1.538 -0.014 1.34e-02 5.57e+03 1.14e+00 bond pdb=" CA ARG C 264 " pdb=" C ARG C 264 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.13e+00 bond pdb=" CA ARG D 264 " pdb=" C ARG D 264 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.11e+00 bond pdb=" CA ARG B 264 " pdb=" C ARG B 264 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.07e+00 ... (remaining 10675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 13928 1.43 - 2.86: 497 2.86 - 4.30: 70 4.30 - 5.73: 25 5.73 - 7.16: 5 Bond angle restraints: 14525 Sorted by residual: angle pdb=" C ARG D 264 " pdb=" N TYR D 265 " pdb=" CA TYR D 265 " ideal model delta sigma weight residual 121.97 126.68 -4.71 1.73e+00 3.34e-01 7.42e+00 angle pdb=" C ARG E 264 " pdb=" N TYR E 265 " pdb=" CA TYR E 265 " ideal model delta sigma weight residual 121.97 126.63 -4.66 1.73e+00 3.34e-01 7.25e+00 angle pdb=" C ARG B 264 " pdb=" N TYR B 265 " pdb=" CA TYR B 265 " ideal model delta sigma weight residual 121.97 126.62 -4.65 1.73e+00 3.34e-01 7.23e+00 angle pdb=" C ARG C 264 " pdb=" N TYR C 265 " pdb=" CA TYR C 265 " ideal model delta sigma weight residual 121.97 126.62 -4.65 1.73e+00 3.34e-01 7.21e+00 angle pdb=" C ARG A 264 " pdb=" N TYR A 265 " pdb=" CA TYR A 265 " ideal model delta sigma weight residual 121.97 126.60 -4.63 1.73e+00 3.34e-01 7.17e+00 ... (remaining 14520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 5640 15.56 - 31.13: 560 31.13 - 46.69: 125 46.69 - 62.25: 45 62.25 - 77.81: 15 Dihedral angle restraints: 6385 sinusoidal: 2465 harmonic: 3920 Sorted by residual: dihedral pdb=" CA ARG B 264 " pdb=" C ARG B 264 " pdb=" N TYR B 265 " pdb=" CA TYR B 265 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG E 264 " pdb=" C ARG E 264 " pdb=" N TYR E 265 " pdb=" CA TYR E 265 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG D 264 " pdb=" C ARG D 264 " pdb=" N TYR D 265 " pdb=" CA TYR D 265 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1298 0.054 - 0.109: 291 0.109 - 0.163: 46 0.163 - 0.217: 0 0.217 - 0.272: 5 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CB VAL B 72 " pdb=" CA VAL B 72 " pdb=" CG1 VAL B 72 " pdb=" CG2 VAL B 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL E 72 " pdb=" CA VAL E 72 " pdb=" CG1 VAL E 72 " pdb=" CG2 VAL E 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL A 72 " pdb=" CA VAL A 72 " pdb=" CG1 VAL A 72 " pdb=" CG2 VAL A 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1637 not shown) Planarity restraints: 1925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 265 " -0.013 2.00e-02 2.50e+03 9.81e-03 1.92e+00 pdb=" CG TYR B 265 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 265 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 265 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 265 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 265 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 265 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 265 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 265 " -0.013 2.00e-02 2.50e+03 9.78e-03 1.91e+00 pdb=" CG TYR C 265 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 265 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 265 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 265 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 265 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 265 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 265 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 265 " 0.013 2.00e-02 2.50e+03 9.77e-03 1.91e+00 pdb=" CG TYR E 265 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR E 265 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 265 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 265 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 265 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 265 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 265 " -0.001 2.00e-02 2.50e+03 ... (remaining 1922 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1738 2.77 - 3.30: 10022 3.30 - 3.83: 17927 3.83 - 4.37: 21197 4.37 - 4.90: 34356 Nonbonded interactions: 85240 Sorted by model distance: nonbonded pdb=" O VAL C 164 " pdb=" OH TYR C 168 " model vdw 2.232 3.040 nonbonded pdb=" O VAL B 164 " pdb=" OH TYR B 168 " model vdw 2.233 3.040 nonbonded pdb=" O VAL E 164 " pdb=" OH TYR E 168 " model vdw 2.233 3.040 nonbonded pdb=" O VAL D 164 " pdb=" OH TYR D 168 " model vdw 2.233 3.040 nonbonded pdb=" O VAL A 164 " pdb=" OH TYR A 168 " model vdw 2.233 3.040 ... (remaining 85235 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.820 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.480 Find NCS groups from input model: 0.090 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 0.032 10680 Z= 0.178 Angle : 0.649 7.159 14525 Z= 0.369 Chirality : 0.048 0.272 1640 Planarity : 0.004 0.033 1925 Dihedral : 14.411 77.814 3865 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.20 (0.23), residues: 1355 helix: 0.22 (0.24), residues: 405 sheet: 1.08 (0.30), residues: 330 loop : -0.35 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 70 TYR 0.024 0.002 TYR B 265 PHE 0.015 0.002 PHE E 82 TRP 0.011 0.002 TRP C 45 HIS 0.003 0.001 HIS D 7 Details of bonding type rmsd covalent geometry : bond 0.00378 (10680) covalent geometry : angle 0.64853 (14525) hydrogen bonds : bond 0.15315 ( 470) hydrogen bonds : angle 7.31814 ( 1350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.410 Fit side-chains REVERT: B 46 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5601 (mm-30) REVERT: C 46 GLU cc_start: 0.5907 (mm-30) cc_final: 0.5346 (mm-30) REVERT: E 46 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5634 (mm-30) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.7856 time to fit residues: 189.1271 Evaluate side-chains 160 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 30 HIS A 71 GLN B 28 GLN B 30 HIS B 71 GLN C 28 GLN C 30 HIS D 28 GLN D 30 HIS D 73 GLN D 207 ASN E 30 HIS E 73 GLN E 207 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.180549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.160339 restraints weight = 9858.083| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 0.69 r_work: 0.3423 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10680 Z= 0.137 Angle : 0.565 10.047 14525 Z= 0.298 Chirality : 0.045 0.187 1640 Planarity : 0.004 0.035 1925 Dihedral : 4.640 17.391 1495 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.62 % Allowed : 7.76 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.00 (0.24), residues: 1355 helix: 1.60 (0.26), residues: 400 sheet: 1.13 (0.30), residues: 335 loop : -0.18 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 264 TYR 0.014 0.001 TYR D 265 PHE 0.012 0.002 PHE B 82 TRP 0.010 0.002 TRP E 45 HIS 0.003 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00303 (10680) covalent geometry : angle 0.56508 (14525) hydrogen bonds : bond 0.04524 ( 470) hydrogen bonds : angle 5.61670 ( 1350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.426 Fit side-chains REVERT: A 46 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6177 (mm-30) REVERT: A 115 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: B 46 GLU cc_start: 0.6430 (mm-30) cc_final: 0.5929 (mm-30) REVERT: B 54 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: B 113 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: B 115 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: B 117 SER cc_start: 0.8748 (t) cc_final: 0.8532 (t) REVERT: B 138 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: B 241 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8270 (mmpt) REVERT: C 25 GLU cc_start: 0.8214 (pp20) cc_final: 0.7918 (tm-30) REVERT: C 46 GLU cc_start: 0.6338 (mm-30) cc_final: 0.5754 (mm-30) REVERT: C 54 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: C 115 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: D 46 GLU cc_start: 0.6428 (mm-30) cc_final: 0.5864 (mm-30) REVERT: D 54 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: E 14 ASP cc_start: 0.8510 (m-30) cc_final: 0.8294 (m-30) REVERT: E 46 GLU cc_start: 0.6344 (mm-30) cc_final: 0.5680 (mm-30) REVERT: E 54 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: E 115 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: E 172 LEU cc_start: 0.8347 (mt) cc_final: 0.8122 (mm) REVERT: E 243 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7564 (mm-30) outliers start: 28 outliers final: 1 residues processed: 196 average time/residue: 0.7759 time to fit residues: 160.6482 Evaluate side-chains 179 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 243 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 30 HIS A 71 GLN B 7 HIS B 71 GLN C 28 GLN C 73 GLN C 207 ASN D 28 GLN D 207 ASN E 30 HIS E 73 GLN E 207 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.180953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.160262 restraints weight = 9868.298| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 0.72 r_work: 0.3430 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10680 Z= 0.124 Angle : 0.529 9.516 14525 Z= 0.277 Chirality : 0.044 0.151 1640 Planarity : 0.004 0.033 1925 Dihedral : 4.511 22.257 1495 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.71 % Allowed : 10.56 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.21 (0.24), residues: 1355 helix: 1.88 (0.27), residues: 405 sheet: 1.35 (0.31), residues: 330 loop : -0.21 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 264 TYR 0.011 0.001 TYR B 265 PHE 0.011 0.001 PHE C 82 TRP 0.008 0.002 TRP E 45 HIS 0.002 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00272 (10680) covalent geometry : angle 0.52905 (14525) hydrogen bonds : bond 0.04261 ( 470) hydrogen bonds : angle 5.34313 ( 1350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.355 Fit side-chains REVERT: A 46 GLU cc_start: 0.6479 (mm-30) cc_final: 0.6092 (mm-30) REVERT: A 115 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: B 24 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8280 (mtmt) REVERT: B 46 GLU cc_start: 0.6409 (mm-30) cc_final: 0.5812 (mm-30) REVERT: B 54 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: B 98 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8129 (m-40) REVERT: B 115 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: B 138 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: B 241 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8265 (mmpt) REVERT: C 25 GLU cc_start: 0.8259 (pp20) cc_final: 0.7972 (tm-30) REVERT: C 46 GLU cc_start: 0.6349 (mm-30) cc_final: 0.5803 (mm-30) REVERT: C 54 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: C 67 MET cc_start: 0.7203 (ttm) cc_final: 0.6808 (tmm) REVERT: C 113 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: C 115 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: D 46 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5683 (mm-30) REVERT: D 54 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: D 115 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: E 46 GLU cc_start: 0.6335 (mm-30) cc_final: 0.5642 (mm-30) REVERT: E 54 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: E 113 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: E 115 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8076 (tt0) outliers start: 29 outliers final: 4 residues processed: 192 average time/residue: 0.8174 time to fit residues: 165.3853 Evaluate side-chains 181 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 7 HIS C 28 GLN C 207 ASN D 7 HIS D 28 GLN D 73 GLN D 193 GLN D 207 ASN E 73 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.179760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.160345 restraints weight = 9893.949| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 0.66 r_work: 0.3420 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10680 Z= 0.138 Angle : 0.527 8.247 14525 Z= 0.280 Chirality : 0.045 0.162 1640 Planarity : 0.004 0.041 1925 Dihedral : 4.655 28.562 1495 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.71 % Allowed : 12.71 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.16 (0.24), residues: 1355 helix: 1.79 (0.26), residues: 405 sheet: 1.28 (0.31), residues: 335 loop : -0.17 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 70 TYR 0.009 0.001 TYR E 265 PHE 0.012 0.002 PHE B 82 TRP 0.007 0.002 TRP C 45 HIS 0.003 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00307 (10680) covalent geometry : angle 0.52733 (14525) hydrogen bonds : bond 0.04442 ( 470) hydrogen bonds : angle 5.31633 ( 1350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.411 Fit side-chains REVERT: B 54 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: B 98 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8180 (m-40) REVERT: B 113 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: B 115 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: B 138 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: B 241 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8275 (mmpt) REVERT: C 24 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8407 (ttmt) REVERT: C 25 GLU cc_start: 0.8315 (pp20) cc_final: 0.8004 (tm-30) REVERT: C 46 GLU cc_start: 0.6432 (mm-30) cc_final: 0.5864 (mm-30) REVERT: C 54 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: C 113 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: C 115 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: D 24 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8427 (mtmt) REVERT: D 46 GLU cc_start: 0.6182 (mm-30) cc_final: 0.5596 (mm-30) REVERT: D 54 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: D 115 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: E 46 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5853 (mm-30) REVERT: E 54 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: E 113 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: E 115 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: E 172 LEU cc_start: 0.8359 (mt) cc_final: 0.8112 (mm) outliers start: 29 outliers final: 4 residues processed: 184 average time/residue: 0.8376 time to fit residues: 162.1707 Evaluate side-chains 181 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 115 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 86 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 7 HIS B 73 GLN C 73 GLN C 193 GLN C 207 ASN D 7 HIS D 28 GLN D 207 ASN E 73 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.177507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.157239 restraints weight = 9840.563| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 0.64 r_work: 0.3317 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10680 Z= 0.186 Angle : 0.572 8.574 14525 Z= 0.307 Chirality : 0.047 0.204 1640 Planarity : 0.005 0.058 1925 Dihedral : 5.071 36.589 1495 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.64 % Allowed : 12.71 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.99 (0.24), residues: 1355 helix: 1.49 (0.26), residues: 410 sheet: 1.25 (0.31), residues: 335 loop : -0.21 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.011 0.001 TYR E 265 PHE 0.015 0.002 PHE D 82 TRP 0.009 0.002 TRP D 45 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00425 (10680) covalent geometry : angle 0.57228 (14525) hydrogen bonds : bond 0.05039 ( 470) hydrogen bonds : angle 5.44067 ( 1350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.444 Fit side-chains REVERT: A 46 GLU cc_start: 0.6419 (mm-30) cc_final: 0.5803 (pt0) REVERT: A 115 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: B 46 GLU cc_start: 0.6442 (mm-30) cc_final: 0.6001 (pt0) REVERT: B 54 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: B 98 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8269 (m-40) REVERT: B 113 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: B 115 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: B 138 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: B 241 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8357 (mmpt) REVERT: C 46 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6253 (mm-30) REVERT: C 54 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: C 113 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: C 115 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: D 46 GLU cc_start: 0.6389 (mm-30) cc_final: 0.5833 (mm-30) REVERT: D 54 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: E 14 ASP cc_start: 0.8693 (m-30) cc_final: 0.8438 (m-30) REVERT: E 46 GLU cc_start: 0.6346 (mm-30) cc_final: 0.5790 (pt0) REVERT: E 54 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: E 113 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: E 115 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: E 172 LEU cc_start: 0.8368 (mt) cc_final: 0.8108 (mm) outliers start: 39 outliers final: 7 residues processed: 189 average time/residue: 0.8324 time to fit residues: 165.7245 Evaluate side-chains 184 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 264 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 193 GLN B 7 HIS B 28 GLN B 193 GLN C 207 ASN D 7 HIS D 28 GLN D 73 GLN D 207 ASN E 28 GLN E 73 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.180468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.158955 restraints weight = 10004.361| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 0.69 r_work: 0.3360 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10680 Z= 0.122 Angle : 0.508 8.826 14525 Z= 0.268 Chirality : 0.044 0.150 1640 Planarity : 0.004 0.034 1925 Dihedral : 4.752 42.114 1495 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.62 % Allowed : 14.02 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.16 (0.24), residues: 1355 helix: 1.80 (0.26), residues: 405 sheet: 1.37 (0.31), residues: 330 loop : -0.23 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 218 TYR 0.016 0.001 TYR D 265 PHE 0.012 0.001 PHE C 82 TRP 0.009 0.002 TRP C 45 HIS 0.002 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00270 (10680) covalent geometry : angle 0.50759 (14525) hydrogen bonds : bond 0.04089 ( 470) hydrogen bonds : angle 5.23440 ( 1350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.429 Fit side-chains REVERT: A 46 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5762 (pt0) REVERT: A 115 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: 3 125 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6501 (ptm160) REVERT: B 46 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6110 (pt0) REVERT: B 54 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: B 98 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8146 (m-40) REVERT: B 113 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: B 115 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: B 241 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8266 (mmpt) REVERT: C 24 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8409 (ttmt) REVERT: C 25 GLU cc_start: 0.8286 (pp20) cc_final: 0.7976 (tm-30) REVERT: C 54 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: C 115 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: D 24 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8442 (mtmt) REVERT: D 46 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5580 (mm-30) REVERT: D 54 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: E 54 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: E 113 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: E 115 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: E 172 LEU cc_start: 0.8296 (mt) cc_final: 0.8070 (mm) outliers start: 28 outliers final: 4 residues processed: 186 average time/residue: 0.8335 time to fit residues: 163.2774 Evaluate side-chains 181 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain 3 residue 125 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 264 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 128 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 38 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 0.0770 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 28 GLN B 7 HIS B 28 GLN C 207 ASN D 7 HIS D 28 GLN D 207 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.183359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.165983 restraints weight = 9844.520| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 0.70 r_work: 0.3423 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10680 Z= 0.100 Angle : 0.485 9.292 14525 Z= 0.254 Chirality : 0.043 0.131 1640 Planarity : 0.004 0.031 1925 Dihedral : 4.493 40.692 1495 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.52 % Allowed : 15.14 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.33 (0.24), residues: 1355 helix: 2.04 (0.26), residues: 405 sheet: 1.42 (0.31), residues: 330 loop : -0.18 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 160 TYR 0.013 0.001 TYR D 265 PHE 0.010 0.001 PHE C 82 TRP 0.008 0.001 TRP E 45 HIS 0.002 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00215 (10680) covalent geometry : angle 0.48538 (14525) hydrogen bonds : bond 0.03650 ( 470) hydrogen bonds : angle 5.11647 ( 1350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.421 Fit side-chains REVERT: A 24 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8275 (mtmt) REVERT: A 115 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: B 24 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8319 (mtmt) REVERT: B 54 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: B 98 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8136 (m-40) REVERT: B 115 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: C 24 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8145 (mtmm) REVERT: C 25 GLU cc_start: 0.8294 (pp20) cc_final: 0.7994 (tm-30) REVERT: C 46 GLU cc_start: 0.6478 (mm-30) cc_final: 0.5885 (mm-30) REVERT: C 54 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: C 115 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: D 22 GLU cc_start: 0.8236 (tt0) cc_final: 0.7998 (tt0) REVERT: D 24 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8339 (mtmm) REVERT: D 46 GLU cc_start: 0.6093 (mm-30) cc_final: 0.5483 (mm-30) REVERT: D 54 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: D 115 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: E 46 GLU cc_start: 0.6269 (mm-30) cc_final: 0.5651 (mm-30) REVERT: E 54 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: E 115 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7930 (tt0) outliers start: 27 outliers final: 4 residues processed: 188 average time/residue: 0.8398 time to fit residues: 166.4384 Evaluate side-chains 175 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 264 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 47 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 67 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 12 optimal weight: 0.0870 chunk 92 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 28 GLN B 7 HIS D 7 HIS D 28 GLN D 207 ASN E 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.182250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.160060 restraints weight = 9951.141| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 0.66 r_work: 0.3381 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10680 Z= 0.101 Angle : 0.478 7.468 14525 Z= 0.253 Chirality : 0.043 0.131 1640 Planarity : 0.004 0.030 1925 Dihedral : 4.434 42.087 1495 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.52 % Allowed : 15.89 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.37 (0.23), residues: 1355 helix: 2.12 (0.26), residues: 405 sheet: 1.41 (0.30), residues: 330 loop : -0.17 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 160 TYR 0.010 0.001 TYR D 265 PHE 0.010 0.001 PHE C 82 TRP 0.007 0.001 TRP E 45 HIS 0.002 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00218 (10680) covalent geometry : angle 0.47777 (14525) hydrogen bonds : bond 0.03649 ( 470) hydrogen bonds : angle 5.08114 ( 1350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.418 Fit side-chains REVERT: A 24 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8286 (mtmt) REVERT: A 115 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: B 24 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8391 (mtmm) REVERT: B 46 GLU cc_start: 0.6379 (mm-30) cc_final: 0.5786 (mm-30) REVERT: B 54 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 98 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: B 115 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: C 24 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8178 (mtmm) REVERT: C 25 GLU cc_start: 0.8330 (pp20) cc_final: 0.8029 (tm-30) REVERT: C 46 GLU cc_start: 0.6523 (mm-30) cc_final: 0.5921 (mm-30) REVERT: C 54 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: C 115 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: D 14 ASP cc_start: 0.8608 (m-30) cc_final: 0.8224 (m-30) REVERT: D 22 GLU cc_start: 0.8251 (tt0) cc_final: 0.8018 (tt0) REVERT: D 24 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8402 (mtmt) REVERT: D 46 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5615 (mm-30) REVERT: D 54 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: D 115 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: E 46 GLU cc_start: 0.6248 (mm-30) cc_final: 0.5540 (mm-30) REVERT: E 54 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: E 113 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: E 115 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7942 (tt0) outliers start: 27 outliers final: 7 residues processed: 188 average time/residue: 0.8197 time to fit residues: 162.3297 Evaluate side-chains 185 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 264 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 3.9990 chunk 113 optimal weight: 0.0670 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 64 optimal weight: 0.2980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 28 GLN B 7 HIS D 7 HIS D 28 GLN D 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.182255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.160766 restraints weight = 9914.872| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 0.70 r_work: 0.3377 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10680 Z= 0.104 Angle : 0.496 11.126 14525 Z= 0.259 Chirality : 0.043 0.131 1640 Planarity : 0.004 0.030 1925 Dihedral : 4.450 41.972 1495 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.15 % Allowed : 16.45 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.40 (0.23), residues: 1355 helix: 2.21 (0.26), residues: 400 sheet: 1.38 (0.30), residues: 330 loop : -0.15 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.009 0.001 TYR D 265 PHE 0.010 0.001 PHE E 82 TRP 0.007 0.001 TRP D 45 HIS 0.002 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00226 (10680) covalent geometry : angle 0.49637 (14525) hydrogen bonds : bond 0.03641 ( 470) hydrogen bonds : angle 5.08369 ( 1350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.403 Fit side-chains REVERT: A 24 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8302 (mtmt) REVERT: A 115 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: B 24 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8412 (mtmm) REVERT: B 46 GLU cc_start: 0.6359 (mm-30) cc_final: 0.5753 (mm-30) REVERT: B 54 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: B 98 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8169 (m-40) REVERT: B 115 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8111 (tt0) REVERT: C 24 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8188 (mtmm) REVERT: C 25 GLU cc_start: 0.8346 (pp20) cc_final: 0.8037 (tm-30) REVERT: C 46 GLU cc_start: 0.6494 (mm-30) cc_final: 0.5922 (mm-30) REVERT: C 54 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: C 115 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: D 14 ASP cc_start: 0.8629 (m-30) cc_final: 0.8237 (m-30) REVERT: D 22 GLU cc_start: 0.8275 (tt0) cc_final: 0.8057 (tt0) REVERT: D 24 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8372 (mtmt) REVERT: D 46 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5617 (mm-30) REVERT: D 54 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: D 115 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: E 46 GLU cc_start: 0.6274 (mm-30) cc_final: 0.5568 (mm-30) REVERT: E 54 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: E 113 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: E 115 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7966 (tt0) outliers start: 23 outliers final: 7 residues processed: 184 average time/residue: 0.8170 time to fit residues: 158.6139 Evaluate side-chains 187 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 24 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 264 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 100 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 28 GLN A 71 GLN B 7 HIS C 7 HIS D 7 HIS D 28 GLN E 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.180367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.161680 restraints weight = 9735.263| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 0.72 r_work: 0.3453 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10680 Z= 0.131 Angle : 0.526 10.338 14525 Z= 0.276 Chirality : 0.044 0.152 1640 Planarity : 0.004 0.035 1925 Dihedral : 4.690 43.891 1495 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.96 % Allowed : 16.82 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.28 (0.23), residues: 1355 helix: 1.98 (0.26), residues: 405 sheet: 1.37 (0.30), residues: 330 loop : -0.18 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.010 0.001 TYR D 265 PHE 0.012 0.002 PHE D 82 TRP 0.006 0.002 TRP E 45 HIS 0.002 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00290 (10680) covalent geometry : angle 0.52648 (14525) hydrogen bonds : bond 0.04198 ( 470) hydrogen bonds : angle 5.18873 ( 1350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.475 Fit side-chains REVERT: A 115 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: B 24 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8303 (mtmt) REVERT: B 54 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: B 98 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8160 (m-40) REVERT: B 115 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: C 25 GLU cc_start: 0.8273 (pp20) cc_final: 0.7973 (tm-30) REVERT: C 54 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: C 115 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: D 24 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8390 (mtmt) REVERT: D 46 GLU cc_start: 0.6165 (mm-30) cc_final: 0.5583 (mm-30) REVERT: D 54 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: D 115 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: E 54 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: E 113 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: E 115 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8076 (tt0) outliers start: 21 outliers final: 8 residues processed: 184 average time/residue: 0.8205 time to fit residues: 159.1436 Evaluate side-chains 186 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 264 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 28 GLN A 71 GLN B 7 HIS C 73 GLN D 7 HIS D 28 GLN E 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.179606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.157181 restraints weight = 9862.454| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 0.69 r_work: 0.3416 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10680 Z= 0.133 Angle : 0.529 9.979 14525 Z= 0.278 Chirality : 0.044 0.157 1640 Planarity : 0.004 0.037 1925 Dihedral : 4.748 45.244 1495 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.96 % Allowed : 17.20 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.25 (0.23), residues: 1355 helix: 1.97 (0.26), residues: 405 sheet: 1.32 (0.30), residues: 330 loop : -0.18 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 40 TYR 0.010 0.001 TYR D 265 PHE 0.012 0.002 PHE B 82 TRP 0.007 0.002 TRP C 45 HIS 0.002 0.001 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00297 (10680) covalent geometry : angle 0.52929 (14525) hydrogen bonds : bond 0.04195 ( 470) hydrogen bonds : angle 5.19760 ( 1350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5370.76 seconds wall clock time: 91 minutes 55.89 seconds (5515.89 seconds total)