Starting phenix.real_space_refine on Sat Aug 23 09:19:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twz_41673/08_2025/8twz_41673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twz_41673/08_2025/8twz_41673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8twz_41673/08_2025/8twz_41673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twz_41673/08_2025/8twz_41673.map" model { file = "/net/cci-nas-00/data/ceres_data/8twz_41673/08_2025/8twz_41673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twz_41673/08_2025/8twz_41673.cif" } resolution = 3.17 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= 0.022 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 20 5.16 5 C 7360 2.51 5 N 1850 2.21 5 O 2040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11270 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2250 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.93, per 1000 atoms: 0.17 Number of scatterers: 11270 At special positions: 0 Unit cell: (89.723, 89.723, 112.424, 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 20 16.00 O 2040 8.00 N 1850 7.00 C 7360 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: 0.99 Conformation dependent library (CDL) restraints added in 299.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2610 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 31.4% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 61 through 70 removed outlier: 4.001A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 222 through 225 removed outlier: 3.682A pdb=" N LEU A 225 " --> pdb=" O VAL A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 284 Processing helix chain 'B' and resid 61 through 70 removed outlier: 4.001A pdb=" N ARG B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 222 through 225 removed outlier: 3.683A pdb=" N LEU B 225 " --> pdb=" O VAL B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 284 Processing helix chain 'C' and resid 61 through 70 removed outlier: 4.002A pdb=" N ARG C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 222 through 225 removed outlier: 3.682A pdb=" N LEU C 225 " --> pdb=" O VAL C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 284 Processing helix chain 'D' and resid 61 through 70 removed outlier: 4.001A pdb=" N ARG D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 222 through 225 removed outlier: 3.682A pdb=" N LEU D 225 " --> pdb=" O VAL D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 284 Processing helix chain 'E' and resid 61 through 70 removed outlier: 4.000A pdb=" N ARG E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 222 through 225 removed outlier: 3.682A pdb=" N LEU E 225 " --> pdb=" O VAL E 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 228 through 248 removed outlier: 4.110A pdb=" N TYR E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 284 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 4.117A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.607A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 147 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE A 20 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 59 removed outlier: 4.118A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.607A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 147 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE B 20 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 59 removed outlier: 4.117A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.607A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL C 147 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE C 20 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 59 removed outlier: 4.117A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.606A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL D 147 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE D 20 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.705A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 59 removed outlier: 4.117A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 59 removed outlier: 3.607A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL E 147 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE E 20 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.706A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.706A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.35 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: 3286 1.34 - 1.45: 2013 1.45 - 1.57: 6246 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 11585 Sorted by residual: bond pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.84e+00 bond pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.83e+00 bond pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.58e+00 ... (remaining 11580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 15085 1.49 - 2.99: 567 2.99 - 4.48: 83 4.48 - 5.97: 29 5.97 - 7.47: 26 Bond angle restraints: 15790 Sorted by residual: angle pdb=" C VAL A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta sigma weight residual 122.64 116.77 5.87 1.77e+00 3.19e-01 1.10e+01 angle pdb=" C VAL C 58 " pdb=" N GLU C 59 " pdb=" CA GLU C 59 " ideal model delta sigma weight residual 122.64 116.77 5.87 1.77e+00 3.19e-01 1.10e+01 angle pdb=" C VAL E 58 " pdb=" N GLU E 59 " pdb=" CA GLU E 59 " ideal model delta sigma weight residual 122.64 116.80 5.84 1.77e+00 3.19e-01 1.09e+01 angle pdb=" C VAL B 58 " pdb=" N GLU B 59 " pdb=" CA GLU B 59 " ideal model delta sigma weight residual 122.64 116.82 5.82 1.77e+00 3.19e-01 1.08e+01 angle pdb=" C VAL D 58 " pdb=" N GLU D 59 " pdb=" CA GLU D 59 " ideal model delta sigma weight residual 122.64 116.82 5.82 1.77e+00 3.19e-01 1.08e+01 ... (remaining 15785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 6041 15.96 - 31.92: 544 31.92 - 47.87: 115 47.87 - 63.83: 40 63.83 - 79.79: 15 Dihedral angle restraints: 6755 sinusoidal: 2715 harmonic: 4040 Sorted by residual: dihedral pdb=" CG ARG B 255 " pdb=" CD ARG B 255 " pdb=" NE ARG B 255 " pdb=" CZ ARG B 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.53 48.47 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG E 255 " pdb=" CD ARG E 255 " pdb=" NE ARG E 255 " pdb=" CZ ARG E 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.54 48.46 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG D 255 " pdb=" CD ARG D 255 " pdb=" NE ARG D 255 " pdb=" CZ ARG D 255 " ideal model delta sinusoidal sigma weight residual 90.00 41.58 48.42 2 1.50e+01 4.44e-03 1.19e+01 ... (remaining 6752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1131 0.041 - 0.082: 399 0.082 - 0.124: 165 0.124 - 0.165: 34 0.165 - 0.206: 11 Chirality restraints: 1740 Sorted by residual: chirality pdb=" CB THR D 149 " pdb=" CA THR D 149 " pdb=" OG1 THR D 149 " pdb=" CG2 THR D 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR C 149 " pdb=" CA THR C 149 " pdb=" OG1 THR C 149 " pdb=" CG2 THR C 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR A 149 " pdb=" CA THR A 149 " pdb=" OG1 THR A 149 " pdb=" CG2 THR A 149 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1737 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 255 " -0.184 9.50e-02 1.11e+02 8.32e-02 5.53e+00 pdb=" NE ARG B 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 255 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 255 " -0.185 9.50e-02 1.11e+02 8.35e-02 5.52e+00 pdb=" NE ARG E 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 255 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 255 " -0.184 9.50e-02 1.11e+02 8.32e-02 5.52e+00 pdb=" NE ARG A 255 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 255 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 255 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 255 " -0.000 2.00e-02 2.50e+03 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3369 2.83 - 3.35: 9583 3.35 - 3.86: 18756 3.86 - 4.38: 21893 4.38 - 4.90: 39594 Nonbonded interactions: 93195 Sorted by model distance: nonbonded pdb=" OH TYR A 245 " pdb=" OH TYR E 270 " model vdw 2.309 3.040 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.329 3.040 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.329 3.040 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.330 3.040 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.330 3.040 ... (remaining 93190 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 0.033 11585 Z= 0.217 Angle : 0.715 7.466 15790 Z= 0.371 Chirality : 0.052 0.206 1740 Planarity : 0.006 0.084 2005 Dihedral : 14.021 79.790 4145 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.22), residues: 1360 helix: -0.43 (0.23), residues: 425 sheet: 0.71 (0.25), residues: 465 loop : -2.01 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG B 255 TYR 0.013 0.001 TYR B 248 PHE 0.009 0.002 PHE E 116 TRP 0.021 0.001 TRP A 206 HIS 0.004 0.001 HIS D 177 Details of bonding type rmsd covalent geometry : bond 0.00426 (11585) covalent geometry : angle 0.71463 (15790) hydrogen bonds : bond 0.14408 ( 530) hydrogen bonds : angle 7.16407 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.334 Fit side-chains REVERT: B 129 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7289 (mt-10) REVERT: C 114 MET cc_start: 0.8537 (ttm) cc_final: 0.8286 (ttm) REVERT: C 263 ASP cc_start: 0.7575 (m-30) cc_final: 0.7285 (m-30) REVERT: D 172 ASP cc_start: 0.8108 (m-30) cc_final: 0.7905 (m-30) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1119 time to fit residues: 29.8087 Evaluate side-chains 170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 89 ASN B 60 ASN B 89 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 89 ASN D 60 ASN D 89 ASN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.142269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.108330 restraints weight = 12588.584| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.88 r_work: 0.2949 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11585 Z= 0.279 Angle : 0.637 7.990 15790 Z= 0.325 Chirality : 0.051 0.141 1740 Planarity : 0.004 0.030 2005 Dihedral : 4.720 17.290 1510 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.13 % Allowed : 10.00 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.23), residues: 1360 helix: 0.89 (0.24), residues: 395 sheet: 0.44 (0.26), residues: 440 loop : -1.69 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 91 TYR 0.016 0.002 TYR E 248 PHE 0.011 0.002 PHE C 19 TRP 0.015 0.002 TRP B 206 HIS 0.005 0.001 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00663 (11585) covalent geometry : angle 0.63736 (15790) hydrogen bonds : bond 0.04253 ( 530) hydrogen bonds : angle 4.86177 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.315 Fit side-chains REVERT: A 60 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8526 (p0) REVERT: A 236 PHE cc_start: 0.7092 (m-80) cc_final: 0.6847 (m-80) REVERT: B 123 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7169 (mpt180) REVERT: C 97 ASP cc_start: 0.8187 (p0) cc_final: 0.7829 (p0) REVERT: D 60 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8640 (p0) REVERT: D 97 ASP cc_start: 0.8266 (p0) cc_final: 0.7830 (p0) REVERT: D 123 ARG cc_start: 0.7854 (ttt90) cc_final: 0.7503 (mtt90) REVERT: D 167 SER cc_start: 0.8674 (m) cc_final: 0.8347 (p) REVERT: D 172 ASP cc_start: 0.8832 (m-30) cc_final: 0.8553 (m-30) REVERT: D 236 PHE cc_start: 0.7035 (m-80) cc_final: 0.6691 (m-80) REVERT: E 60 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8571 (p0) REVERT: E 159 GLU cc_start: 0.7708 (pm20) cc_final: 0.7482 (pm20) REVERT: E 167 SER cc_start: 0.8809 (m) cc_final: 0.8326 (p) REVERT: E 236 PHE cc_start: 0.7188 (m-80) cc_final: 0.6962 (m-80) outliers start: 14 outliers final: 7 residues processed: 203 average time/residue: 0.1173 time to fit residues: 32.9677 Evaluate side-chains 176 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 169 HIS C 60 ASN D 60 ASN E 60 ASN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.144769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.112048 restraints weight = 12611.170| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.83 r_work: 0.2988 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11585 Z= 0.142 Angle : 0.552 9.144 15790 Z= 0.279 Chirality : 0.047 0.143 1740 Planarity : 0.003 0.023 2005 Dihedral : 4.314 15.054 1510 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.45 % Allowed : 12.26 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.23), residues: 1360 helix: 1.32 (0.25), residues: 390 sheet: 0.98 (0.27), residues: 415 loop : -1.87 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 123 TYR 0.019 0.001 TYR D 245 PHE 0.009 0.001 PHE B 116 TRP 0.018 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00325 (11585) covalent geometry : angle 0.55151 (15790) hydrogen bonds : bond 0.03566 ( 530) hydrogen bonds : angle 4.44664 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.437 Fit side-chains REVERT: B 114 MET cc_start: 0.8360 (ttm) cc_final: 0.7992 (ttm) REVERT: B 123 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7087 (mpt180) REVERT: B 245 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7236 (t80) REVERT: C 245 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7248 (t80) REVERT: C 255 ARG cc_start: 0.8273 (mtt90) cc_final: 0.7958 (mtt90) REVERT: D 97 ASP cc_start: 0.8324 (p0) cc_final: 0.7926 (p0) REVERT: D 123 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7358 (mpt180) REVERT: D 137 ASN cc_start: 0.8835 (p0) cc_final: 0.8560 (p0) REVERT: D 167 SER cc_start: 0.8603 (m) cc_final: 0.8369 (p) REVERT: D 172 ASP cc_start: 0.8823 (m-30) cc_final: 0.8515 (m-30) REVERT: E 167 SER cc_start: 0.8683 (m) cc_final: 0.8307 (p) outliers start: 18 outliers final: 8 residues processed: 192 average time/residue: 0.1059 time to fit residues: 28.9653 Evaluate side-chains 165 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 56 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 122 optimal weight: 0.0670 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN C 21 ASN C 60 ASN C 169 HIS D 169 HIS E 169 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.146580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.114212 restraints weight = 12565.728| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.84 r_work: 0.3188 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11585 Z= 0.110 Angle : 0.512 8.623 15790 Z= 0.259 Chirality : 0.046 0.140 1740 Planarity : 0.003 0.023 2005 Dihedral : 4.016 13.798 1510 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.61 % Allowed : 14.03 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.23), residues: 1360 helix: 1.54 (0.25), residues: 390 sheet: 1.06 (0.27), residues: 415 loop : -1.87 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 255 TYR 0.017 0.001 TYR D 245 PHE 0.008 0.001 PHE E 236 TRP 0.018 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00248 (11585) covalent geometry : angle 0.51193 (15790) hydrogen bonds : bond 0.03223 ( 530) hydrogen bonds : angle 4.16217 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.457 Fit side-chains REVERT: A 245 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7527 (t80) REVERT: B 114 MET cc_start: 0.8599 (ttm) cc_final: 0.8097 (ttm) REVERT: B 245 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7540 (t80) REVERT: C 27 ASN cc_start: 0.8291 (t0) cc_final: 0.7976 (t0) REVERT: C 34 LYS cc_start: 0.8839 (mttp) cc_final: 0.8599 (mttt) REVERT: C 59 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8288 (mm-30) REVERT: C 61 THR cc_start: 0.8544 (t) cc_final: 0.8253 (p) REVERT: C 245 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7076 (t80) REVERT: D 97 ASP cc_start: 0.8296 (p0) cc_final: 0.7849 (p0) REVERT: D 172 ASP cc_start: 0.8747 (m-30) cc_final: 0.8491 (m-30) REVERT: E 167 SER cc_start: 0.8675 (m) cc_final: 0.8470 (p) REVERT: E 245 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7472 (t80) outliers start: 20 outliers final: 10 residues processed: 178 average time/residue: 0.0990 time to fit residues: 25.5665 Evaluate side-chains 171 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 1 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN C 21 ASN C 60 ASN D 21 ASN D 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.146748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.112013 restraints weight = 12549.236| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.11 r_work: 0.3107 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11585 Z= 0.115 Angle : 0.512 7.323 15790 Z= 0.256 Chirality : 0.046 0.138 1740 Planarity : 0.003 0.023 2005 Dihedral : 3.923 13.281 1510 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.77 % Allowed : 15.00 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.23), residues: 1360 helix: 1.61 (0.25), residues: 390 sheet: 1.10 (0.27), residues: 415 loop : -1.86 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 255 TYR 0.017 0.001 TYR D 245 PHE 0.016 0.001 PHE E 236 TRP 0.018 0.001 TRP D 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00261 (11585) covalent geometry : angle 0.51154 (15790) hydrogen bonds : bond 0.03154 ( 530) hydrogen bonds : angle 4.08110 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7093 (t80) REVERT: B 245 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7424 (t80) REVERT: C 34 LYS cc_start: 0.8901 (mttp) cc_final: 0.8660 (mttt) REVERT: C 245 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7095 (t80) REVERT: D 172 ASP cc_start: 0.8761 (m-30) cc_final: 0.8526 (m-30) REVERT: E 167 SER cc_start: 0.8685 (m) cc_final: 0.8446 (p) REVERT: E 236 PHE cc_start: 0.7309 (m-80) cc_final: 0.7068 (m-80) REVERT: E 245 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7127 (t80) outliers start: 22 outliers final: 14 residues processed: 179 average time/residue: 0.1141 time to fit residues: 29.0371 Evaluate side-chains 166 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.146445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112852 restraints weight = 12542.701| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.97 r_work: 0.3011 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11585 Z= 0.118 Angle : 0.512 8.705 15790 Z= 0.256 Chirality : 0.046 0.136 1740 Planarity : 0.003 0.022 2005 Dihedral : 3.882 13.139 1510 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.77 % Allowed : 15.89 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.23), residues: 1360 helix: 1.66 (0.25), residues: 390 sheet: 1.09 (0.27), residues: 415 loop : -1.84 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 255 TYR 0.014 0.001 TYR E 245 PHE 0.011 0.001 PHE E 236 TRP 0.017 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00266 (11585) covalent geometry : angle 0.51238 (15790) hydrogen bonds : bond 0.03113 ( 530) hydrogen bonds : angle 4.03551 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.6976 (t80) REVERT: B 239 MET cc_start: 0.7452 (tpp) cc_final: 0.7112 (ttp) REVERT: B 245 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7282 (t80) REVERT: C 34 LYS cc_start: 0.8842 (mttp) cc_final: 0.8592 (mttt) REVERT: C 245 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7006 (t80) REVERT: D 137 ASN cc_start: 0.8868 (p0) cc_final: 0.8544 (p0) REVERT: D 172 ASP cc_start: 0.8766 (m-30) cc_final: 0.8454 (m-30) REVERT: E 167 SER cc_start: 0.8734 (m) cc_final: 0.8417 (p) REVERT: E 245 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7032 (t80) outliers start: 22 outliers final: 17 residues processed: 178 average time/residue: 0.1129 time to fit residues: 28.5579 Evaluate side-chains 172 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 87 optimal weight: 0.2980 chunk 58 optimal weight: 0.0070 chunk 89 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.0770 chunk 118 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN C 60 ASN D 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.147305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114102 restraints weight = 12477.877| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.97 r_work: 0.3203 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11585 Z= 0.101 Angle : 0.501 7.753 15790 Z= 0.249 Chirality : 0.046 0.136 1740 Planarity : 0.003 0.021 2005 Dihedral : 3.797 12.766 1510 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.02 % Allowed : 16.21 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.23), residues: 1360 helix: 1.70 (0.25), residues: 390 sheet: 1.12 (0.27), residues: 415 loop : -1.81 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 255 TYR 0.013 0.001 TYR E 245 PHE 0.021 0.001 PHE B 236 TRP 0.018 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00223 (11585) covalent geometry : angle 0.50065 (15790) hydrogen bonds : bond 0.02972 ( 530) hydrogen bonds : angle 3.96377 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7031 (t80) REVERT: B 239 MET cc_start: 0.7663 (tpp) cc_final: 0.7309 (ttp) REVERT: B 245 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7263 (t80) REVERT: C 34 LYS cc_start: 0.8888 (mttp) cc_final: 0.8648 (mttt) REVERT: C 245 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7048 (t80) REVERT: D 137 ASN cc_start: 0.8895 (p0) cc_final: 0.8574 (p0) REVERT: D 172 ASP cc_start: 0.8673 (m-30) cc_final: 0.8355 (m-30) REVERT: D 233 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6178 (tt0) REVERT: E 59 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8238 (mm-30) REVERT: E 236 PHE cc_start: 0.7327 (m-80) cc_final: 0.7065 (m-80) REVERT: E 245 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7065 (t80) outliers start: 25 outliers final: 19 residues processed: 183 average time/residue: 0.1110 time to fit residues: 29.1379 Evaluate side-chains 185 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN D 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.145109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112859 restraints weight = 12513.158| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.81 r_work: 0.2997 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11585 Z= 0.152 Angle : 0.534 7.510 15790 Z= 0.267 Chirality : 0.047 0.134 1740 Planarity : 0.003 0.020 2005 Dihedral : 3.939 14.079 1510 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.18 % Allowed : 16.53 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.23), residues: 1360 helix: 1.66 (0.25), residues: 390 sheet: 1.05 (0.27), residues: 415 loop : -1.84 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.014 0.001 TYR E 245 PHE 0.012 0.001 PHE B 236 TRP 0.018 0.001 TRP B 206 HIS 0.003 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00353 (11585) covalent geometry : angle 0.53443 (15790) hydrogen bonds : bond 0.03229 ( 530) hydrogen bonds : angle 4.06394 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.423 Fit side-chains REVERT: A 245 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6931 (t80) REVERT: B 59 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7966 (mm-30) REVERT: B 123 ARG cc_start: 0.7767 (mtp85) cc_final: 0.6950 (mpt180) REVERT: B 239 MET cc_start: 0.7430 (tpp) cc_final: 0.7080 (ttp) REVERT: B 245 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7204 (t80) REVERT: C 30 GLU cc_start: 0.7482 (tt0) cc_final: 0.7264 (tt0) REVERT: C 34 LYS cc_start: 0.8849 (mttp) cc_final: 0.8609 (mttt) REVERT: C 245 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.6961 (t80) REVERT: D 137 ASN cc_start: 0.8899 (p0) cc_final: 0.8624 (p0) REVERT: D 172 ASP cc_start: 0.8741 (m-30) cc_final: 0.8479 (m-30) REVERT: D 233 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.6093 (tt0) REVERT: D 255 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.8278 (mtt90) REVERT: E 236 PHE cc_start: 0.7194 (m-80) cc_final: 0.6926 (m-80) REVERT: E 245 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.6697 (t80) outliers start: 27 outliers final: 22 residues processed: 181 average time/residue: 0.1238 time to fit residues: 31.4359 Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 44 optimal weight: 0.0020 chunk 32 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.147549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.114639 restraints weight = 12414.386| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.95 r_work: 0.3035 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11585 Z= 0.099 Angle : 0.505 7.480 15790 Z= 0.251 Chirality : 0.046 0.136 1740 Planarity : 0.003 0.020 2005 Dihedral : 3.781 13.315 1510 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.34 % Allowed : 16.94 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.23), residues: 1360 helix: 1.74 (0.25), residues: 390 sheet: 1.09 (0.27), residues: 415 loop : -1.80 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.013 0.001 TYR A 245 PHE 0.009 0.001 PHE E 236 TRP 0.017 0.001 TRP B 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00217 (11585) covalent geometry : angle 0.50539 (15790) hydrogen bonds : bond 0.02938 ( 530) hydrogen bonds : angle 3.92372 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8147 (mm-30) REVERT: A 236 PHE cc_start: 0.7110 (m-80) cc_final: 0.6821 (m-80) REVERT: A 245 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6967 (t80) REVERT: B 239 MET cc_start: 0.7393 (tpp) cc_final: 0.7049 (ttp) REVERT: B 245 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7074 (t80) REVERT: C 27 ASN cc_start: 0.8182 (t0) cc_final: 0.7727 (t0) REVERT: C 34 LYS cc_start: 0.8820 (mttp) cc_final: 0.8572 (mttt) REVERT: C 59 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 245 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6971 (t80) REVERT: D 59 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8210 (mm-30) REVERT: D 137 ASN cc_start: 0.8818 (p0) cc_final: 0.8534 (p0) REVERT: D 172 ASP cc_start: 0.8749 (m-30) cc_final: 0.8451 (m-30) REVERT: D 233 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.6019 (tt0) REVERT: D 236 PHE cc_start: 0.7124 (m-10) cc_final: 0.6795 (m-80) REVERT: D 255 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.8247 (mtt90) REVERT: E 236 PHE cc_start: 0.7196 (m-80) cc_final: 0.6917 (m-80) REVERT: E 245 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.6732 (t80) outliers start: 29 outliers final: 22 residues processed: 188 average time/residue: 0.1165 time to fit residues: 31.2718 Evaluate side-chains 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 125 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.146450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.112967 restraints weight = 12556.511| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.98 r_work: 0.3017 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11585 Z= 0.123 Angle : 0.521 7.937 15790 Z= 0.258 Chirality : 0.046 0.134 1740 Planarity : 0.003 0.020 2005 Dihedral : 3.809 13.569 1510 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.26 % Allowed : 16.77 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.24), residues: 1360 helix: 1.73 (0.25), residues: 390 sheet: 1.10 (0.27), residues: 415 loop : -1.81 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.014 0.001 TYR A 245 PHE 0.009 0.001 PHE E 236 TRP 0.018 0.001 TRP B 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00279 (11585) covalent geometry : angle 0.52087 (15790) hydrogen bonds : bond 0.03047 ( 530) hydrogen bonds : angle 3.94490 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8099 (mm-30) REVERT: A 236 PHE cc_start: 0.6986 (m-80) cc_final: 0.6714 (m-80) REVERT: A 245 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.6948 (t80) REVERT: B 159 GLU cc_start: 0.7643 (pm20) cc_final: 0.7360 (pm20) REVERT: B 239 MET cc_start: 0.7371 (tpp) cc_final: 0.7028 (ttp) REVERT: B 245 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7094 (t80) REVERT: C 34 LYS cc_start: 0.8841 (mttp) cc_final: 0.8606 (mttt) REVERT: C 245 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.6994 (t80) REVERT: D 59 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8264 (mm-30) REVERT: D 137 ASN cc_start: 0.8891 (p0) cc_final: 0.8669 (p0) REVERT: D 172 ASP cc_start: 0.8749 (m-30) cc_final: 0.8483 (m-30) REVERT: D 233 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.6011 (tt0) REVERT: D 236 PHE cc_start: 0.7061 (m-10) cc_final: 0.6745 (m-80) REVERT: D 255 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8257 (mtt90) REVERT: E 236 PHE cc_start: 0.7167 (m-80) cc_final: 0.6892 (m-80) REVERT: E 245 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6732 (t80) outliers start: 28 outliers final: 22 residues processed: 180 average time/residue: 0.1088 time to fit residues: 27.6863 Evaluate side-chains 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 30 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 0.0870 chunk 95 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.148517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114264 restraints weight = 12573.069| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.06 r_work: 0.3024 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11585 Z= 0.101 Angle : 0.506 8.355 15790 Z= 0.250 Chirality : 0.046 0.135 1740 Planarity : 0.003 0.020 2005 Dihedral : 3.712 13.342 1510 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.18 % Allowed : 17.02 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.24), residues: 1360 helix: 1.76 (0.25), residues: 390 sheet: 1.15 (0.27), residues: 415 loop : -1.79 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.013 0.001 TYR A 245 PHE 0.009 0.001 PHE E 236 TRP 0.017 0.001 TRP B 206 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00224 (11585) covalent geometry : angle 0.50579 (15790) hydrogen bonds : bond 0.02888 ( 530) hydrogen bonds : angle 3.85693 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.35 seconds wall clock time: 46 minutes 47.33 seconds (2807.33 seconds total)