Starting phenix.real_space_refine on Tue Jul 29 06:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twz_41673/07_2025/8twz_41673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twz_41673/07_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_41673/07_2025/8twz_41673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twz_41673/07_2025/8twz_41673.map" model { file = "/net/cci-nas-00/data/ceres_data/8twz_41673/07_2025/8twz_41673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twz_41673/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 4.87, per 1000 atoms: 0.43 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: 3.18 Conformation dependent library (CDL) restraints added in 1.3 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: 1.60 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: 3.77 Time building geometry restraints manager: 3.61 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: 0.370 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 27.020 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- 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 : 1.355 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: 0.2601 time to fit residues: 69.0732 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 : 1.377 ------------------------------------------------------------------------------- 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: 0.7980 chunk 122 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 D 60 ASN D 89 ASN D 233 GLN E 60 ASN E 89 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.150195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117113 restraints weight = 12393.940| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.92 r_work: 0.3182 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11585 Z= 0.108 Angle : 0.511 5.926 15790 Z= 0.257 Chirality : 0.046 0.128 1740 Planarity : 0.003 0.021 2005 Dihedral : 4.111 14.756 1510 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.77 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: 1.03 (0.24), residues: 395 sheet: 0.83 (0.27), residues: 445 loop : -1.76 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.001 0.000 HIS C 177 PHE 0.015 0.001 PHE B 236 TYR 0.011 0.001 TYR C 245 ARG 0.003 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 530) hydrogen bonds : angle 4.56950 ( 1800) covalent geometry : bond 0.00244 (11585) covalent geometry : angle 0.51056 (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 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 1.327 Fit side-chains REVERT: B 114 MET cc_start: 0.8600 (ttm) cc_final: 0.8103 (ttm) REVERT: B 129 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 236 PHE cc_start: 0.7409 (m-80) cc_final: 0.7171 (m-80) REVERT: C 86 ASP cc_start: 0.7791 (t0) cc_final: 0.7526 (t0) REVERT: C 174 ARG cc_start: 0.8339 (ttm110) cc_final: 0.7764 (ttm-80) REVERT: D 86 ASP cc_start: 0.7807 (t0) cc_final: 0.7579 (t0) REVERT: D 150 GLU cc_start: 0.6769 (pt0) cc_final: 0.6287 (mt-10) REVERT: D 172 ASP cc_start: 0.8760 (m-30) cc_final: 0.8396 (m-30) REVERT: D 255 ARG cc_start: 0.8504 (mtt-85) cc_final: 0.8187 (mtt90) REVERT: E 167 SER cc_start: 0.8697 (m) cc_final: 0.8413 (p) outliers start: 10 outliers final: 8 residues processed: 184 average time/residue: 0.2354 time to fit residues: 62.1391 Evaluate side-chains 146 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3530 r_free = 0.3530 target = 0.142680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.109639 restraints weight = 12679.320| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.83 r_work: 0.2956 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 11585 Z= 0.277 Angle : 0.633 11.305 15790 Z= 0.323 Chirality : 0.051 0.148 1740 Planarity : 0.004 0.023 2005 Dihedral : 4.444 15.021 1510 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.45 % Allowed : 11.05 % Favored : 87.50 % 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: 0.06 (0.23), residues: 1360 helix: 1.20 (0.25), residues: 395 sheet: 1.14 (0.27), residues: 415 loop : -1.79 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 206 HIS 0.004 0.001 HIS C 177 PHE 0.014 0.002 PHE E 236 TYR 0.017 0.002 TYR C 245 ARG 0.005 0.001 ARG E 91 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 530) hydrogen bonds : angle 4.61263 ( 1800) covalent geometry : bond 0.00662 (11585) covalent geometry : angle 0.63257 (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 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.241 Fit side-chains REVERT: B 123 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7132 (mpt180) REVERT: B 245 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7251 (t80) REVERT: C 59 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8129 (mm-30) REVERT: C 245 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7131 (t80) REVERT: D 86 ASP cc_start: 0.7653 (t0) cc_final: 0.7369 (t0) REVERT: D 172 ASP cc_start: 0.8769 (m-30) cc_final: 0.8488 (m-30) REVERT: E 30 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: E 167 SER cc_start: 0.8729 (m) cc_final: 0.8301 (p) REVERT: E 215 ILE cc_start: 0.7450 (mm) cc_final: 0.7241 (mt) outliers start: 18 outliers final: 10 residues processed: 189 average time/residue: 0.2809 time to fit residues: 72.4916 Evaluate side-chains 166 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 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 241 THR Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 167 SER 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: 2.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN C 60 ASN C 89 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 = 0.3567 r_free = 0.3567 target = 0.146019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.112499 restraints weight = 12476.605| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.98 r_work: 0.3012 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11585 Z= 0.119 Angle : 0.514 8.047 15790 Z= 0.258 Chirality : 0.047 0.140 1740 Planarity : 0.003 0.026 2005 Dihedral : 4.058 14.786 1510 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.10 % Allowed : 13.55 % 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 (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: 0.17 (0.23), residues: 1360 helix: 1.49 (0.25), residues: 390 sheet: 1.22 (0.27), residues: 415 loop : -1.88 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.022 0.001 PHE E 236 TYR 0.017 0.001 TYR A 245 ARG 0.006 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 530) hydrogen bonds : angle 4.22992 ( 1800) covalent geometry : bond 0.00274 (11585) covalent geometry : angle 0.51404 (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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.564 Fit side-chains REVERT: B 30 GLU cc_start: 0.7088 (tt0) cc_final: 0.6844 (tt0) REVERT: B 107 LEU cc_start: 0.8753 (tt) cc_final: 0.8509 (tt) REVERT: B 245 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.6996 (t80) REVERT: C 59 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8104 (mm-30) REVERT: C 245 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7050 (t80) REVERT: D 86 ASP cc_start: 0.7628 (t0) cc_final: 0.7345 (t0) REVERT: D 172 ASP cc_start: 0.8784 (m-30) cc_final: 0.8494 (m-30) REVERT: E 30 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: E 167 SER cc_start: 0.8697 (m) cc_final: 0.8366 (p) outliers start: 26 outliers final: 11 residues processed: 184 average time/residue: 0.2798 time to fit residues: 72.6423 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 : 1.284 ------------------------------------------------------------------------------- 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 245 TYR Chi-restraints excluded: chain C residue 56 LEU 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 D residue 97 ASP Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 109 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 65 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN D 233 GLN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.145262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.111652 restraints weight = 12454.062| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.94 r_work: 0.2997 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11585 Z= 0.139 Angle : 0.529 8.922 15790 Z= 0.267 Chirality : 0.047 0.139 1740 Planarity : 0.003 0.031 2005 Dihedral : 3.993 15.062 1510 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.77 % Allowed : 14.44 % Favored : 83.79 % 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: 0.19 (0.24), residues: 1360 helix: 1.58 (0.25), residues: 390 sheet: 1.18 (0.27), residues: 415 loop : -1.88 (0.26), residues: 555 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 0.022 0.001 PHE E 236 TYR 0.017 0.001 TYR D 245 ARG 0.005 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 530) hydrogen bonds : angle 4.17917 ( 1800) covalent geometry : bond 0.00321 (11585) covalent geometry : angle 0.52862 (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 197 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 1.278 Fit side-chains REVERT: A 245 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.6980 (t80) REVERT: B 123 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7076 (mpt180) REVERT: B 239 MET cc_start: 0.7519 (tpp) cc_final: 0.7193 (ttp) REVERT: B 245 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.6862 (t80) REVERT: C 59 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8167 (mm-30) REVERT: C 245 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6964 (t80) REVERT: D 27 ASN cc_start: 0.8234 (t0) cc_final: 0.8029 (t0) REVERT: D 86 ASP cc_start: 0.7600 (t0) cc_final: 0.7257 (t0) REVERT: D 172 ASP cc_start: 0.8765 (m-30) cc_final: 0.8465 (m-30) REVERT: D 255 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8316 (mtt90) REVERT: E 30 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: E 167 SER cc_start: 0.8731 (m) cc_final: 0.8389 (p) outliers start: 22 outliers final: 13 residues processed: 189 average time/residue: 0.2558 time to fit residues: 67.3131 Evaluate side-chains 179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 61 THR 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 240 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.147157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.113626 restraints weight = 12608.780| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.95 r_work: 0.3024 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11585 Z= 0.106 Angle : 0.503 7.720 15790 Z= 0.251 Chirality : 0.046 0.137 1740 Planarity : 0.003 0.033 2005 Dihedral : 3.825 14.467 1510 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.10 % Allowed : 14.60 % Favored : 83.31 % 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: 0.26 (0.24), residues: 1360 helix: 1.67 (0.25), residues: 390 sheet: 1.17 (0.27), residues: 415 loop : -1.82 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.023 0.001 PHE E 236 TYR 0.016 0.001 TYR E 245 ARG 0.006 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 530) hydrogen bonds : angle 4.02629 ( 1800) covalent geometry : bond 0.00237 (11585) covalent geometry : angle 0.50279 (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 200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 167 SER cc_start: 0.8693 (m) cc_final: 0.8436 (t) REVERT: A 245 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.6933 (t80) REVERT: B 123 ARG cc_start: 0.7767 (mtp85) cc_final: 0.6957 (mpt180) REVERT: B 239 MET cc_start: 0.7427 (tpp) cc_final: 0.7083 (ttp) REVERT: B 245 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7016 (t80) REVERT: C 34 LYS cc_start: 0.8786 (mttp) cc_final: 0.8525 (mttt) REVERT: C 245 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7082 (t80) REVERT: D 86 ASP cc_start: 0.7647 (t0) cc_final: 0.7352 (t0) REVERT: D 172 ASP cc_start: 0.8755 (m-30) cc_final: 0.8462 (m-30) REVERT: D 233 GLN cc_start: 0.6334 (OUTLIER) cc_final: 0.5807 (tt0) REVERT: D 255 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.8299 (mtt90) REVERT: E 167 SER cc_start: 0.8705 (m) cc_final: 0.8394 (p) REVERT: E 245 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.6984 (t80) outliers start: 26 outliers final: 17 residues processed: 191 average time/residue: 0.2662 time to fit residues: 71.3819 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 : 1.247 ------------------------------------------------------------------------------- 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 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 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 167 SER Chi-restraints excluded: chain D residue 233 GLN 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: 8.9990 chunk 117 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.143441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.109684 restraints weight = 12774.375| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.87 r_work: 0.2967 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11585 Z= 0.196 Angle : 0.566 7.178 15790 Z= 0.285 Chirality : 0.048 0.138 1740 Planarity : 0.003 0.039 2005 Dihedral : 4.131 16.153 1510 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.02 % Allowed : 15.97 % Favored : 82.02 % 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: 0.13 (0.24), residues: 1360 helix: 1.49 (0.25), residues: 395 sheet: 1.18 (0.27), residues: 410 loop : -1.92 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 206 HIS 0.003 0.001 HIS C 177 PHE 0.020 0.001 PHE E 236 TYR 0.017 0.001 TYR E 245 ARG 0.009 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 530) hydrogen bonds : angle 4.25795 ( 1800) covalent geometry : bond 0.00460 (11585) covalent geometry : angle 0.56553 (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 189 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.365 Fit side-chains REVERT: A 245 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.6889 (t80) REVERT: B 123 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7098 (mpt180) REVERT: B 239 MET cc_start: 0.7702 (tpp) cc_final: 0.7369 (ttp) REVERT: B 245 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6835 (t80) REVERT: C 240 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7771 (tt) REVERT: C 245 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6940 (t80) REVERT: D 86 ASP cc_start: 0.7658 (t0) cc_final: 0.7287 (t0) REVERT: D 172 ASP cc_start: 0.8750 (m-30) cc_final: 0.8460 (m-30) REVERT: D 233 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6134 (tt0) REVERT: D 255 ARG cc_start: 0.8563 (mtt-85) cc_final: 0.8329 (mtt90) REVERT: E 167 SER cc_start: 0.8770 (m) cc_final: 0.8418 (p) REVERT: E 245 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.6753 (t80) outliers start: 25 outliers final: 16 residues processed: 181 average time/residue: 0.2692 time to fit residues: 67.8675 Evaluate side-chains 182 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 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 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 240 LEU 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 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 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: 2.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.112875 restraints weight = 12584.966| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.97 r_work: 0.3011 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2216 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= 0.113 Angle : 0.519 7.769 15790 Z= 0.258 Chirality : 0.046 0.138 1740 Planarity : 0.003 0.035 2005 Dihedral : 3.867 15.263 1510 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.10 % Allowed : 16.53 % Favored : 81.37 % 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: 0.19 (0.23), residues: 1360 helix: 1.65 (0.25), residues: 390 sheet: 1.19 (0.27), residues: 410 loop : -1.91 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 206 HIS 0.002 0.001 HIS B 177 PHE 0.019 0.001 PHE E 236 TYR 0.015 0.001 TYR E 245 ARG 0.007 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 530) hydrogen bonds : angle 4.06928 ( 1800) covalent geometry : bond 0.00251 (11585) covalent geometry : angle 0.51859 (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: 26 poor density : 165 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 167 SER cc_start: 0.8697 (m) cc_final: 0.8446 (t) REVERT: A 245 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6884 (t80) REVERT: B 239 MET cc_start: 0.7517 (tpp) cc_final: 0.7136 (ttp) REVERT: B 245 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.6863 (t80) REVERT: C 34 LYS cc_start: 0.8803 (mttp) cc_final: 0.8538 (mttt) REVERT: C 59 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7994 (mm-30) REVERT: C 245 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6953 (t80) REVERT: D 30 GLU cc_start: 0.7407 (tt0) cc_final: 0.7182 (tt0) REVERT: D 86 ASP cc_start: 0.7659 (t0) cc_final: 0.7358 (t0) REVERT: D 172 ASP cc_start: 0.8746 (m-30) cc_final: 0.8477 (m-30) REVERT: D 233 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6032 (tt0) REVERT: D 255 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8301 (mtt90) REVERT: E 167 SER cc_start: 0.8695 (m) cc_final: 0.8409 (p) REVERT: E 245 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.6719 (t80) outliers start: 26 outliers final: 20 residues processed: 184 average time/residue: 0.2684 time to fit residues: 69.1441 Evaluate side-chains 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 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 97 ASP 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 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: 1.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 ASN D 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.147498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.113905 restraints weight = 12615.626| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.99 r_work: 0.3023 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2240 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= 0.108 Angle : 0.521 9.301 15790 Z= 0.256 Chirality : 0.046 0.136 1740 Planarity : 0.003 0.032 2005 Dihedral : 3.788 14.777 1510 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.02 % Allowed : 17.18 % 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 (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: 0.25 (0.24), residues: 1360 helix: 1.69 (0.25), residues: 390 sheet: 1.24 (0.27), residues: 410 loop : -1.88 (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 A 177 PHE 0.017 0.001 PHE E 236 TYR 0.014 0.001 TYR E 245 ARG 0.007 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 530) hydrogen bonds : angle 3.97167 ( 1800) covalent geometry : bond 0.00241 (11585) covalent geometry : angle 0.52086 (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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 3.119 Fit side-chains revert: symmetry clash REVERT: A 167 SER cc_start: 0.8704 (m) cc_final: 0.8446 (t) REVERT: A 236 PHE cc_start: 0.6925 (m-80) cc_final: 0.6676 (m-80) REVERT: A 245 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.6891 (t80) REVERT: B 61 THR cc_start: 0.8197 (t) cc_final: 0.7679 (p) REVERT: B 159 GLU cc_start: 0.7643 (pm20) cc_final: 0.7391 (pm20) REVERT: B 239 MET cc_start: 0.7371 (tpp) cc_final: 0.7028 (ttp) REVERT: B 245 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.6931 (t80) REVERT: C 27 ASN cc_start: 0.8244 (t0) cc_final: 0.7735 (t0) REVERT: C 34 LYS cc_start: 0.8811 (mttp) cc_final: 0.8561 (mttt) REVERT: C 59 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8019 (mm-30) REVERT: C 245 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7004 (t80) REVERT: D 59 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8240 (mm-30) REVERT: D 86 ASP cc_start: 0.7630 (t0) cc_final: 0.7383 (t0) REVERT: D 172 ASP cc_start: 0.8741 (m-30) cc_final: 0.8484 (m-30) REVERT: D 233 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.6021 (tt0) REVERT: D 255 ARG cc_start: 0.8501 (mtt-85) cc_final: 0.8248 (mtt90) REVERT: E 167 SER cc_start: 0.8686 (m) cc_final: 0.8396 (p) REVERT: E 245 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.6610 (t80) outliers start: 25 outliers final: 20 residues processed: 185 average time/residue: 0.3712 time to fit residues: 96.6901 Evaluate side-chains 182 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 2.107 ------------------------------------------------------------------------------- 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 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 97 ASP 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 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 26 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 48 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 28 optimal weight: 0.2980 chunk 102 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN C 169 HIS D 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.148656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.114602 restraints weight = 12509.503| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.95 r_work: 0.3035 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2313 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= 0.099 Angle : 0.507 8.500 15790 Z= 0.250 Chirality : 0.046 0.134 1740 Planarity : 0.003 0.036 2005 Dihedral : 3.662 14.350 1510 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.26 % Allowed : 17.02 % 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 (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: 0.31 (0.24), residues: 1360 helix: 1.74 (0.25), residues: 390 sheet: 1.28 (0.27), residues: 410 loop : -1.85 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 206 HIS 0.002 0.001 HIS D 177 PHE 0.017 0.001 PHE E 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 0.02879 ( 530) hydrogen bonds : angle 3.86750 ( 1800) covalent geometry : bond 0.00218 (11585) covalent geometry : angle 0.50657 (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 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 1.729 Fit side-chains revert: symmetry clash REVERT: A 167 SER cc_start: 0.8686 (m) cc_final: 0.8420 (t) REVERT: A 236 PHE cc_start: 0.6840 (m-80) cc_final: 0.6596 (m-80) REVERT: A 245 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.6887 (t80) REVERT: B 61 THR cc_start: 0.8041 (t) cc_final: 0.7646 (p) REVERT: B 236 PHE cc_start: 0.7132 (m-80) cc_final: 0.6844 (m-80) REVERT: B 239 MET cc_start: 0.7223 (tpp) cc_final: 0.6914 (ttp) REVERT: B 245 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7098 (t80) REVERT: C 27 ASN cc_start: 0.8162 (t0) cc_final: 0.7634 (t0) REVERT: C 34 LYS cc_start: 0.8792 (mttp) cc_final: 0.8542 (mttt) REVERT: C 245 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7058 (t80) REVERT: D 59 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8272 (mm-30) REVERT: D 86 ASP cc_start: 0.7616 (t0) cc_final: 0.7363 (t0) REVERT: D 172 ASP cc_start: 0.8778 (m-30) cc_final: 0.8516 (m-30) REVERT: D 233 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.5940 (tt0) REVERT: D 255 ARG cc_start: 0.8476 (mtt-85) cc_final: 0.8230 (mtt90) REVERT: E 167 SER cc_start: 0.8651 (m) cc_final: 0.8340 (p) REVERT: E 245 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.6636 (t80) outliers start: 28 outliers final: 21 residues processed: 182 average time/residue: 0.3292 time to fit residues: 84.0541 Evaluate side-chains 170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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 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 97 ASP 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 24 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.143448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.109729 restraints weight = 12639.499| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.94 r_work: 0.3149 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11585 Z= 0.203 Angle : 0.577 7.554 15790 Z= 0.288 Chirality : 0.048 0.138 1740 Planarity : 0.003 0.052 2005 Dihedral : 4.084 16.803 1510 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.26 % Allowed : 17.18 % Favored : 80.56 % 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: 1.56 (0.26), residues: 395 sheet: 1.16 (0.27), residues: 410 loop : -1.91 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 206 HIS 0.004 0.001 HIS C 177 PHE 0.017 0.001 PHE E 236 TYR 0.017 0.002 TYR E 245 ARG 0.009 0.001 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 530) hydrogen bonds : angle 4.15670 ( 1800) covalent geometry : bond 0.00475 (11585) covalent geometry : angle 0.57704 (15790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6228.82 seconds wall clock time: 111 minutes 12.84 seconds (6672.84 seconds total)