Starting phenix.real_space_refine on Tue May 13 23:26:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twz_41673/05_2025/8twz_41673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twz_41673/05_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_41673/05_2025/8twz_41673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twz_41673/05_2025/8twz_41673.map" model { file = "/net/cci-nas-00/data/ceres_data/8twz_41673/05_2025/8twz_41673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twz_41673/05_2025/8twz_41673.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D Time building chain proxies: 4.66, per 1000 atoms: 0.41 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: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.59 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: 3.81 Time building geometry restraints manager: 3.33 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.250 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.460 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.690 ------------------------------------------------------------------------------- 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 : 5.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.001 TRP A 206 HIS 0.004 0.001 HIS D 177 PHE 0.009 0.002 PHE E 116 TYR 0.013 0.001 TYR B 248 ARG 0.020 0.002 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.14408 ( 530) hydrogen bonds : angle 7.16407 ( 1800) covalent geometry : bond 0.00426 (11585) covalent geometry : angle 0.71463 (15790) *********************** 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 : 1.286 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: 0.2527 time to fit residues: 67.1558 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 : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 69 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 122 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 169 HIS B 233 GLN C 60 ASN C 89 ASN D 60 ASN D 89 ASN D 233 GLN E 60 ASN E 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.149987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.116681 restraints weight = 12401.312| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.93 r_work: 0.3070 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11585 Z= 0.108 Angle : 0.511 5.937 15790 Z= 0.258 Chirality : 0.046 0.133 1740 Planarity : 0.003 0.020 2005 Dihedral : 4.134 14.964 1510 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.81 % Allowed : 7.74 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.23), residues: 1360 helix: 1.04 (0.24), residues: 395 sheet: 0.79 (0.27), residues: 445 loop : -1.73 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.001 0.001 HIS C 177 PHE 0.015 0.001 PHE B 236 TYR 0.010 0.001 TYR B 245 ARG 0.003 0.001 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 530) hydrogen bonds : angle 4.60479 ( 1800) covalent geometry : bond 0.00244 (11585) covalent geometry : angle 0.51107 (15790) *********************** 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 182 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 1.182 Fit side-chains REVERT: B 129 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8078 (mt-10) REVERT: B 236 PHE cc_start: 0.7224 (m-80) cc_final: 0.6962 (m-80) REVERT: C 86 ASP cc_start: 0.7734 (t0) cc_final: 0.7503 (t0) REVERT: C 114 MET cc_start: 0.8390 (ttm) cc_final: 0.8190 (ttm) REVERT: C 174 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7614 (ttm-80) REVERT: D 86 ASP cc_start: 0.7771 (t0) cc_final: 0.7568 (t0) REVERT: D 150 GLU cc_start: 0.6765 (pt0) cc_final: 0.6253 (mt-10) REVERT: D 167 SER cc_start: 0.8469 (m) cc_final: 0.8225 (p) REVERT: D 172 ASP cc_start: 0.8815 (m-30) cc_final: 0.8467 (m-30) REVERT: D 255 ARG cc_start: 0.8394 (mtt-85) cc_final: 0.8029 (mtt90) REVERT: E 159 GLU cc_start: 0.7624 (pm20) cc_final: 0.7407 (pm20) REVERT: E 167 SER cc_start: 0.8695 (m) cc_final: 0.8288 (p) outliers start: 10 outliers final: 8 residues processed: 182 average time/residue: 0.2380 time to fit residues: 62.6083 Evaluate side-chains 154 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 60 ASN Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 60 ASN 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 28 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 60 ASN C 60 ASN D 60 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.144069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110218 restraints weight = 12636.318| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.86 r_work: 0.2975 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11585 Z= 0.218 Angle : 0.585 7.657 15790 Z= 0.297 Chirality : 0.049 0.154 1740 Planarity : 0.003 0.022 2005 Dihedral : 4.270 14.492 1510 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.53 % Allowed : 10.65 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1360 helix: 1.29 (0.25), residues: 395 sheet: 0.68 (0.26), residues: 440 loop : -1.59 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.003 0.001 HIS B 169 PHE 0.014 0.002 PHE E 236 TYR 0.016 0.002 TYR C 245 ARG 0.004 0.000 ARG E 91 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 530) hydrogen bonds : angle 4.51149 ( 1800) covalent geometry : bond 0.00517 (11585) covalent geometry : angle 0.58517 (15790) *********************** 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 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.356 Fit side-chains REVERT: B 123 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7121 (mpt180) REVERT: B 245 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7212 (t80) REVERT: C 34 LYS cc_start: 0.8832 (mttp) cc_final: 0.8575 (mttt) REVERT: C 245 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7182 (t80) REVERT: D 86 ASP cc_start: 0.7673 (t0) cc_final: 0.7405 (t0) REVERT: D 167 SER cc_start: 0.8608 (m) cc_final: 0.8283 (p) REVERT: D 172 ASP cc_start: 0.8801 (m-30) cc_final: 0.8508 (m-30) REVERT: E 30 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: E 167 SER cc_start: 0.8747 (m) cc_final: 0.8309 (p) REVERT: E 215 ILE cc_start: 0.7399 (mm) cc_final: 0.7169 (mt) outliers start: 19 outliers final: 8 residues processed: 185 average time/residue: 0.2731 time to fit residues: 69.5281 Evaluate side-chains 165 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 30 GLU 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 102 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 109 optimal weight: 0.0050 chunk 26 optimal weight: 6.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.145864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.112294 restraints weight = 12514.587| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.95 r_work: 0.3007 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11585 Z= 0.126 Angle : 0.518 9.921 15790 Z= 0.261 Chirality : 0.047 0.141 1740 Planarity : 0.003 0.023 2005 Dihedral : 4.040 14.417 1510 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.69 % Allowed : 13.63 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1360 helix: 1.54 (0.25), residues: 390 sheet: 1.22 (0.27), residues: 415 loop : -1.85 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 206 HIS 0.002 0.001 HIS B 169 PHE 0.023 0.001 PHE E 236 TYR 0.019 0.001 TYR D 245 ARG 0.007 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 530) hydrogen bonds : angle 4.21865 ( 1800) covalent geometry : bond 0.00291 (11585) covalent geometry : angle 0.51774 (15790) *********************** 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 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 1.166 Fit side-chains REVERT: B 107 LEU cc_start: 0.8762 (tt) cc_final: 0.8540 (tt) REVERT: B 245 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7221 (t80) REVERT: C 34 LYS cc_start: 0.8822 (mttp) cc_final: 0.8556 (mttt) REVERT: C 59 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8168 (mm-30) REVERT: C 245 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7251 (t80) REVERT: D 86 ASP cc_start: 0.7643 (t0) cc_final: 0.7368 (t0) REVERT: D 167 SER cc_start: 0.8586 (m) cc_final: 0.8307 (p) REVERT: D 172 ASP cc_start: 0.8767 (m-30) cc_final: 0.8500 (m-30) REVERT: E 30 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: E 167 SER cc_start: 0.8668 (m) cc_final: 0.8303 (p) outliers start: 21 outliers final: 11 residues processed: 181 average time/residue: 0.2350 time to fit residues: 60.5801 Evaluate side-chains 168 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 180 SER 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 245 TYR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 240 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 109 optimal weight: 0.0570 chunk 133 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 0.0170 chunk 100 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 16 optimal weight: 0.0020 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS E 169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.148217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.116282 restraints weight = 12435.378| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.83 r_work: 0.3045 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11585 Z= 0.100 Angle : 0.496 8.990 15790 Z= 0.250 Chirality : 0.046 0.141 1740 Planarity : 0.003 0.021 2005 Dihedral : 3.801 12.807 1510 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.69 % Allowed : 13.63 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1360 helix: 1.66 (0.25), residues: 390 sheet: 1.22 (0.27), residues: 415 loop : -1.80 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 206 HIS 0.002 0.001 HIS C 177 PHE 0.022 0.001 PHE E 236 TYR 0.015 0.001 TYR A 245 ARG 0.004 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 530) hydrogen bonds : angle 4.00460 ( 1800) covalent geometry : bond 0.00221 (11585) covalent geometry : angle 0.49600 (15790) *********************** 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 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 245 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7433 (t80) REVERT: B 107 LEU cc_start: 0.8675 (tt) cc_final: 0.8474 (tt) REVERT: B 114 MET cc_start: 0.8313 (ttm) cc_final: 0.7838 (ttm) REVERT: B 239 MET cc_start: 0.7381 (tpp) cc_final: 0.7027 (ttp) REVERT: B 245 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7391 (t80) REVERT: C 27 ASN cc_start: 0.7987 (t0) cc_final: 0.7583 (t0) REVERT: C 34 LYS cc_start: 0.8805 (mttp) cc_final: 0.8571 (mttt) REVERT: C 167 SER cc_start: 0.8586 (m) cc_final: 0.8236 (p) REVERT: C 245 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7171 (t80) REVERT: D 86 ASP cc_start: 0.7603 (t0) cc_final: 0.7308 (t0) REVERT: D 167 SER cc_start: 0.8568 (m) cc_final: 0.8338 (p) REVERT: D 172 ASP cc_start: 0.8754 (m-30) cc_final: 0.8477 (m-30) REVERT: E 30 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: E 167 SER cc_start: 0.8707 (m) cc_final: 0.8394 (p) REVERT: E 245 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6989 (t80) outliers start: 21 outliers final: 11 residues processed: 185 average time/residue: 0.2396 time to fit residues: 63.2235 Evaluate side-chains 176 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 THR 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 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU 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 129 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 100 optimal weight: 0.0000 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN D 21 ASN D 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.146954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114988 restraints weight = 12633.388| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.79 r_work: 0.3028 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2034 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= 0.119 Angle : 0.510 7.847 15790 Z= 0.255 Chirality : 0.047 0.137 1740 Planarity : 0.003 0.020 2005 Dihedral : 3.816 13.166 1510 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.85 % Allowed : 14.03 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1360 helix: 1.66 (0.25), residues: 390 sheet: 1.21 (0.27), residues: 415 loop : -1.80 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 206 HIS 0.002 0.001 HIS A 177 PHE 0.008 0.001 PHE B 116 TYR 0.015 0.001 TYR D 245 ARG 0.004 0.000 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 530) hydrogen bonds : angle 4.00860 ( 1800) covalent geometry : bond 0.00271 (11585) covalent geometry : angle 0.50985 (15790) *********************** 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 180 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 123 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7333 (mtp85) REVERT: A 245 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.6998 (t80) REVERT: B 114 MET cc_start: 0.8383 (ttm) cc_final: 0.7915 (ttm) REVERT: B 123 ARG cc_start: 0.7766 (mtp85) cc_final: 0.6960 (mpt180) REVERT: B 239 MET cc_start: 0.7385 (tpp) cc_final: 0.7024 (ttp) REVERT: B 245 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7313 (t80) REVERT: C 34 LYS cc_start: 0.8817 (mttp) cc_final: 0.8588 (mttt) REVERT: C 245 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7113 (t80) REVERT: D 86 ASP cc_start: 0.7624 (t0) cc_final: 0.7290 (t0) REVERT: D 167 SER cc_start: 0.8608 (m) cc_final: 0.8346 (p) REVERT: D 172 ASP cc_start: 0.8753 (m-30) cc_final: 0.8512 (m-30) REVERT: E 30 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: E 167 SER cc_start: 0.8724 (m) cc_final: 0.8386 (p) REVERT: E 245 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.6866 (t80) outliers start: 23 outliers final: 17 residues processed: 171 average time/residue: 0.2682 time to fit residues: 63.4234 Evaluate side-chains 175 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 28 THR 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 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 240 LEU 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 86 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.146086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.113496 restraints weight = 12695.967| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.86 r_work: 0.3010 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11585 Z= 0.132 Angle : 0.516 7.242 15790 Z= 0.259 Chirality : 0.047 0.136 1740 Planarity : 0.003 0.036 2005 Dihedral : 3.874 13.828 1510 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.94 % Allowed : 14.44 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.24), residues: 1360 helix: 1.65 (0.25), residues: 390 sheet: 1.19 (0.27), residues: 415 loop : -1.79 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 206 HIS 0.002 0.001 HIS B 169 PHE 0.008 0.001 PHE B 116 TYR 0.015 0.001 TYR E 245 ARG 0.008 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03107 ( 530) hydrogen bonds : angle 4.03465 ( 1800) covalent geometry : bond 0.00305 (11585) covalent geometry : angle 0.51608 (15790) *********************** 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 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.118 Fit side-chains REVERT: A 123 ARG cc_start: 0.7623 (mtt90) cc_final: 0.7365 (mtp85) REVERT: A 245 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6949 (t80) REVERT: B 114 MET cc_start: 0.8437 (ttm) cc_final: 0.7964 (ttm) REVERT: B 123 ARG cc_start: 0.7790 (mtp85) cc_final: 0.6939 (mpt180) REVERT: B 239 MET cc_start: 0.7427 (tpp) cc_final: 0.7069 (ttp) REVERT: B 245 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7284 (t80) REVERT: C 34 LYS cc_start: 0.8839 (mttp) cc_final: 0.8612 (mttt) REVERT: C 59 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8230 (mm-30) REVERT: C 245 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7142 (t80) REVERT: D 86 ASP cc_start: 0.7650 (t0) cc_final: 0.7320 (t0) REVERT: D 167 SER cc_start: 0.8621 (m) cc_final: 0.8351 (p) REVERT: D 172 ASP cc_start: 0.8764 (m-30) cc_final: 0.8468 (m-30) REVERT: D 255 ARG cc_start: 0.8547 (mtt-85) cc_final: 0.8293 (mtt90) REVERT: E 30 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: E 59 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8282 (mm-30) REVERT: E 167 SER cc_start: 0.8730 (m) cc_final: 0.8387 (p) REVERT: E 245 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.6725 (t80) outliers start: 24 outliers final: 16 residues processed: 177 average time/residue: 0.2545 time to fit residues: 62.3237 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 : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU 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 28 THR 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 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 240 LEU 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 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.146181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.112280 restraints weight = 12605.990| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.99 r_work: 0.3005 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11585 Z= 0.140 Angle : 0.526 7.762 15790 Z= 0.264 Chirality : 0.047 0.135 1740 Planarity : 0.003 0.043 2005 Dihedral : 3.898 14.329 1510 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.85 % Allowed : 15.24 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1360 helix: 1.64 (0.25), residues: 390 sheet: 1.15 (0.27), residues: 415 loop : -1.80 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 206 HIS 0.003 0.001 HIS B 169 PHE 0.008 0.001 PHE B 116 TYR 0.015 0.001 TYR E 245 ARG 0.009 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 530) hydrogen bonds : angle 4.04970 ( 1800) covalent geometry : bond 0.00323 (11585) covalent geometry : angle 0.52611 (15790) *********************** 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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.238 Fit side-chains REVERT: A 123 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7365 (mtp85) REVERT: A 245 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6875 (t80) REVERT: B 61 THR cc_start: 0.8278 (t) cc_final: 0.7838 (p) REVERT: B 114 MET cc_start: 0.8407 (ttm) cc_final: 0.7956 (ttm) REVERT: B 239 MET cc_start: 0.7368 (tpp) cc_final: 0.6986 (ttp) REVERT: B 245 TYR cc_start: 0.7956 (OUTLIER) cc_final: 0.7123 (t80) REVERT: C 34 LYS cc_start: 0.8848 (mttp) cc_final: 0.8623 (mttt) REVERT: C 59 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 245 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7112 (t80) REVERT: D 86 ASP cc_start: 0.7643 (t0) cc_final: 0.7313 (t0) REVERT: D 167 SER cc_start: 0.8625 (m) cc_final: 0.8338 (p) REVERT: D 172 ASP cc_start: 0.8777 (m-30) cc_final: 0.8501 (m-30) REVERT: D 233 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6005 (tt0) REVERT: D 255 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8335 (mtt90) REVERT: E 30 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: E 167 SER cc_start: 0.8654 (m) cc_final: 0.8302 (p) REVERT: E 245 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6566 (t80) outliers start: 23 outliers final: 16 residues processed: 183 average time/residue: 0.2550 time to fit residues: 65.2528 Evaluate side-chains 181 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU 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 28 THR 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 143 SER Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU 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 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.147231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115129 restraints weight = 12616.744| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.82 r_work: 0.3200 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2193 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= 0.110 Angle : 0.510 7.566 15790 Z= 0.255 Chirality : 0.046 0.137 1740 Planarity : 0.003 0.040 2005 Dihedral : 3.778 14.134 1510 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.18 % Allowed : 14.92 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1360 helix: 1.67 (0.25), residues: 390 sheet: 1.16 (0.27), residues: 415 loop : -1.77 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 206 HIS 0.002 0.001 HIS A 177 PHE 0.019 0.001 PHE B 236 TYR 0.014 0.001 TYR E 245 ARG 0.008 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 530) hydrogen bonds : angle 3.96608 ( 1800) covalent geometry : bond 0.00247 (11585) covalent geometry : angle 0.50968 (15790) *********************** 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 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.215 Fit side-chains REVERT: A 236 PHE cc_start: 0.7268 (m-80) cc_final: 0.7022 (m-80) REVERT: A 245 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7079 (t80) REVERT: B 61 THR cc_start: 0.8285 (t) cc_final: 0.7879 (p) REVERT: B 236 PHE cc_start: 0.7414 (m-80) cc_final: 0.7108 (m-80) REVERT: B 239 MET cc_start: 0.7670 (tpp) cc_final: 0.7289 (ttp) REVERT: B 245 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7297 (t80) REVERT: C 34 LYS cc_start: 0.8884 (mttp) cc_final: 0.8666 (mttt) REVERT: C 59 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8339 (mm-30) REVERT: C 245 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7191 (t80) REVERT: D 30 GLU cc_start: 0.7362 (tt0) cc_final: 0.7112 (tt0) REVERT: D 86 ASP cc_start: 0.7762 (t0) cc_final: 0.7523 (t0) REVERT: D 172 ASP cc_start: 0.8670 (m-30) cc_final: 0.8393 (m-30) REVERT: D 233 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.6176 (tt0) REVERT: D 255 ARG cc_start: 0.8610 (mtt-85) cc_final: 0.8386 (mtt90) REVERT: E 30 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: E 245 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.6691 (t80) outliers start: 27 outliers final: 20 residues processed: 178 average time/residue: 0.2466 time to fit residues: 61.3276 Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 180 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain B residue 28 THR 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 245 TYR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 180 SER 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 26 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.144301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.111876 restraints weight = 12611.211| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.82 r_work: 0.2985 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11585 Z= 0.174 Angle : 0.557 7.314 15790 Z= 0.279 Chirality : 0.048 0.137 1740 Planarity : 0.003 0.043 2005 Dihedral : 4.055 15.944 1510 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.10 % Allowed : 15.40 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1360 helix: 1.59 (0.25), residues: 390 sheet: 1.17 (0.27), residues: 410 loop : -1.93 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 206 HIS 0.003 0.001 HIS D 177 PHE 0.019 0.001 PHE B 236 TYR 0.016 0.001 TYR E 245 ARG 0.008 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 530) hydrogen bonds : angle 4.15900 ( 1800) covalent geometry : bond 0.00406 (11585) covalent geometry : angle 0.55658 (15790) ********************** 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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.258 Fit side-chains REVERT: A 245 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.6929 (t80) REVERT: B 123 ARG cc_start: 0.7787 (mtp85) cc_final: 0.6951 (mpt180) REVERT: B 239 MET cc_start: 0.7547 (tpp) cc_final: 0.7182 (ttp) REVERT: B 245 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.6915 (t80) REVERT: C 34 LYS cc_start: 0.8843 (mttp) cc_final: 0.8613 (mttt) REVERT: C 59 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8338 (mm-30) REVERT: C 245 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6968 (t80) REVERT: D 30 GLU cc_start: 0.7262 (tt0) cc_final: 0.7027 (tt0) REVERT: D 86 ASP cc_start: 0.7613 (t0) cc_final: 0.7329 (t0) REVERT: D 172 ASP cc_start: 0.8743 (m-30) cc_final: 0.8456 (m-30) REVERT: D 233 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6034 (tt0) REVERT: D 255 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8327 (mtt90) REVERT: E 30 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: E 245 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6533 (t80) outliers start: 26 outliers final: 19 residues processed: 182 average time/residue: 0.2470 time to fit residues: 62.7915 Evaluate side-chains 189 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE 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 28 THR 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 245 TYR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 233 GLN Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 180 SER 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 24 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 0.0470 chunk 67 optimal weight: 1.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 ASN E 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.146191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.114274 restraints weight = 12551.442| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.82 r_work: 0.3017 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2269 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= 0.117 Angle : 0.523 7.007 15790 Z= 0.260 Chirality : 0.046 0.138 1740 Planarity : 0.003 0.041 2005 Dihedral : 3.864 15.232 1510 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.18 % Allowed : 15.40 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.23), residues: 1360 helix: 1.64 (0.25), residues: 390 sheet: 1.20 (0.27), residues: 410 loop : -1.87 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.008 0.001 PHE E 236 TYR 0.014 0.001 TYR A 245 ARG 0.008 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 530) hydrogen bonds : angle 4.02310 ( 1800) covalent geometry : bond 0.00265 (11585) covalent geometry : angle 0.52270 (15790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5748.27 seconds wall clock time: 99 minutes 59.55 seconds (5999.55 seconds total)