Starting phenix.real_space_refine on Mon Nov 17 19:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwx_21425/11_2025/6vwx_21425_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwx_21425/11_2025/6vwx_21425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vwx_21425/11_2025/6vwx_21425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwx_21425/11_2025/6vwx_21425.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwx_21425/11_2025/6vwx_21425_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwx_21425/11_2025/6vwx_21425_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 24 5.16 5 Na 2 4.78 5 C 5336 2.51 5 N 1188 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7782 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "E" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' NA': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, F Time building chain proxies: 2.09, per 1000 atoms: 0.27 Number of scatterers: 7782 At special positions: 0 Unit cell: (121.426, 121.426, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 8 15.00 Na 2 11.00 O 1224 8.00 N 1188 7.00 C 5336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 433.3 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 removed outlier: 3.811A pdb=" N THR A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 55 through 77 removed outlier: 3.881A pdb=" N ALA A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.750A pdb=" N TRP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.670A pdb=" N ARG A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.513A pdb=" N ARG A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 164 removed outlier: 3.763A pdb=" N LEU A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.558A pdb=" N VAL A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.724A pdb=" N GLU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 237 removed outlier: 3.507A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 43 removed outlier: 3.812A pdb=" N THR D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 55 through 77 removed outlier: 3.882A pdb=" N ALA D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 103 removed outlier: 3.750A pdb=" N TRP D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 122 removed outlier: 3.670A pdb=" N ARG D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.512A pdb=" N ARG D 132 " --> pdb=" O PRO D 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 133 " --> pdb=" O SER D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 164 removed outlier: 3.763A pdb=" N LEU D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.558A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.724A pdb=" N GLU D 204 " --> pdb=" O PRO D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 237 removed outlier: 3.506A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 43 removed outlier: 3.812A pdb=" N THR E 26 " --> pdb=" O HIS E 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 55 through 77 removed outlier: 3.881A pdb=" N ALA E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 103 removed outlier: 3.751A pdb=" N TRP E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 122 removed outlier: 3.670A pdb=" N ARG E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 127 through 139 removed outlier: 3.513A pdb=" N ARG E 132 " --> pdb=" O PRO E 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 164 removed outlier: 3.763A pdb=" N LEU E 148 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE E 149 " --> pdb=" O GLY E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 189 removed outlier: 3.558A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.725A pdb=" N GLU E 204 " --> pdb=" O PRO E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 237 removed outlier: 3.507A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 43 removed outlier: 3.811A pdb=" N THR F 26 " --> pdb=" O HIS F 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE F 27 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU F 43 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 52 Processing helix chain 'F' and resid 55 through 77 removed outlier: 3.881A pdb=" N ALA F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 103 removed outlier: 3.750A pdb=" N TRP F 91 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 removed outlier: 3.670A pdb=" N ARG F 113 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 127 through 139 removed outlier: 3.513A pdb=" N ARG F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 164 removed outlier: 3.763A pdb=" N LEU F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE F 149 " --> pdb=" O GLY F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 189 removed outlier: 3.559A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 189 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.725A pdb=" N GLU F 204 " --> pdb=" O PRO F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 237 removed outlier: 3.506A pdb=" N PHE F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 223 " --> pdb=" O GLY F 219 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1052 1.30 - 1.43: 2291 1.43 - 1.55: 4540 1.55 - 1.68: 57 1.68 - 1.81: 48 Bond restraints: 7988 Sorted by residual: bond pdb=" C31 POV F 302 " pdb=" O31 POV F 302 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C31 POV A 301 " pdb=" O31 POV A 301 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C31 POV D 301 " pdb=" O31 POV D 301 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C31 POV E 302 " pdb=" O31 POV E 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C21 POV E 302 " pdb=" O21 POV E 302 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 7983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 10259 2.39 - 4.79: 367 4.79 - 7.18: 114 7.18 - 9.58: 44 9.58 - 11.97: 20 Bond angle restraints: 10804 Sorted by residual: angle pdb=" C ASN E 79 " pdb=" N PRO E 80 " pdb=" CA PRO E 80 " ideal model delta sigma weight residual 119.84 131.81 -11.97 1.25e+00 6.40e-01 9.18e+01 angle pdb=" C ASN F 79 " pdb=" N PRO F 80 " pdb=" CA PRO F 80 " ideal model delta sigma weight residual 119.84 131.81 -11.97 1.25e+00 6.40e-01 9.17e+01 angle pdb=" C ASN A 79 " pdb=" N PRO A 80 " pdb=" CA PRO A 80 " ideal model delta sigma weight residual 119.84 131.78 -11.94 1.25e+00 6.40e-01 9.13e+01 angle pdb=" C ASN D 79 " pdb=" N PRO D 80 " pdb=" CA PRO D 80 " ideal model delta sigma weight residual 119.84 131.78 -11.94 1.25e+00 6.40e-01 9.12e+01 angle pdb=" N VAL E 197 " pdb=" CA VAL E 197 " pdb=" C VAL E 197 " ideal model delta sigma weight residual 110.72 118.38 -7.66 1.01e+00 9.80e-01 5.75e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 3948 23.68 - 47.37: 544 47.37 - 71.05: 136 71.05 - 94.73: 36 94.73 - 118.41: 4 Dihedral angle restraints: 4668 sinusoidal: 2020 harmonic: 2648 Sorted by residual: dihedral pdb=" C29 POV E 302 " pdb="C210 POV E 302 " pdb="C211 POV E 302 " pdb="C212 POV E 302 " ideal model delta sinusoidal sigma weight residual 112.25 -129.34 -118.41 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C29 POV A 301 " pdb="C210 POV A 301 " pdb="C211 POV A 301 " pdb="C212 POV A 301 " ideal model delta sinusoidal sigma weight residual 112.25 -129.35 -118.40 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C29 POV D 301 " pdb="C210 POV D 301 " pdb="C211 POV D 301 " pdb="C212 POV D 301 " ideal model delta sinusoidal sigma weight residual 112.25 -129.36 -118.39 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 935 0.052 - 0.104: 261 0.104 - 0.156: 32 0.156 - 0.209: 0 0.209 - 0.261: 4 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CA MET E 198 " pdb=" N MET E 198 " pdb=" C MET E 198 " pdb=" CB MET E 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET F 198 " pdb=" N MET F 198 " pdb=" C MET F 198 " pdb=" CB MET F 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET A 198 " pdb=" N MET A 198 " pdb=" C MET A 198 " pdb=" CB MET A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1229 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 199 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO F 200 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 199 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 200 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 199 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.52e+00 pdb=" N PRO E 200 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 200 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 200 " 0.037 5.00e-02 4.00e+02 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1122 2.74 - 3.28: 7813 3.28 - 3.82: 12303 3.82 - 4.36: 14717 4.36 - 4.90: 24876 Nonbonded interactions: 60831 Sorted by model distance: nonbonded pdb=" O SER D 78 " pdb=" OG SER D 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER F 78 " pdb=" OG SER F 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER E 78 " pdb=" OG SER E 78 " model vdw 2.201 3.040 nonbonded pdb=" O PHE A 158 " pdb=" OH TYR A 211 " model vdw 2.277 3.040 ... (remaining 60826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 13 through 302) selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.650 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.011 0.098 7988 Z= 0.507 Angle : 1.291 11.973 10804 Z= 0.639 Chirality : 0.047 0.261 1232 Planarity : 0.006 0.064 1256 Dihedral : 22.960 118.414 2940 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.07 % Favored : 91.48 % Rotamer: Outliers : 15.83 % Allowed : 15.83 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.22), residues: 892 helix: -2.52 (0.15), residues: 644 sheet: None (None), residues: 0 loop : -3.55 (0.32), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.007 0.001 TYR D 156 PHE 0.012 0.001 PHE D 174 TRP 0.006 0.001 TRP A 91 HIS 0.001 0.000 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.01056 ( 7988) covalent geometry : angle 1.29073 (10804) hydrogen bonds : bond 0.20341 ( 428) hydrogen bonds : angle 8.81949 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 175 time to evaluate : 0.310 Fit side-chains REVERT: A 22 HIS cc_start: 0.7582 (t-90) cc_final: 0.7250 (t-90) REVERT: A 90 ASN cc_start: 0.8947 (m110) cc_final: 0.8691 (m110) REVERT: A 95 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 191 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7978 (tm-30) REVERT: D 22 HIS cc_start: 0.7639 (t-90) cc_final: 0.7290 (t70) REVERT: D 90 ASN cc_start: 0.8931 (m110) cc_final: 0.8659 (m110) REVERT: D 95 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8485 (tp) REVERT: D 191 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7768 (tm-30) REVERT: E 22 HIS cc_start: 0.7651 (t-90) cc_final: 0.7286 (t70) REVERT: E 70 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: E 90 ASN cc_start: 0.8910 (m110) cc_final: 0.8649 (m110) REVERT: E 122 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8431 (ttt-90) REVERT: E 181 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8958 (tt) REVERT: E 191 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7766 (tm-30) REVERT: F 22 HIS cc_start: 0.7615 (t-90) cc_final: 0.7264 (t70) REVERT: F 53 LYS cc_start: 0.8029 (tptp) cc_final: 0.7808 (tptp) REVERT: F 90 ASN cc_start: 0.8934 (m110) cc_final: 0.8685 (m110) REVERT: F 191 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7911 (tm-30) outliers start: 126 outliers final: 83 residues processed: 263 average time/residue: 0.0773 time to fit residues: 28.8097 Evaluate side-chains 248 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 160 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 235 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 167 GLN A 186 GLN A 234 ASN D 90 ASN D 167 GLN D 186 GLN D 234 ASN E 90 ASN E 167 GLN E 186 GLN E 234 ASN F 90 ASN F 167 GLN F 186 GLN F 234 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.136404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101924 restraints weight = 11878.410| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.98 r_work: 0.3164 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7988 Z= 0.150 Angle : 0.613 10.615 10804 Z= 0.316 Chirality : 0.040 0.195 1232 Planarity : 0.006 0.056 1256 Dihedral : 21.603 108.361 1477 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.17 % Favored : 92.38 % Rotamer: Outliers : 8.67 % Allowed : 18.59 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.27), residues: 892 helix: -0.34 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.006 0.001 TYR D 156 PHE 0.015 0.001 PHE F 215 TRP 0.022 0.001 TRP D 54 HIS 0.001 0.000 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7988) covalent geometry : angle 0.61308 (10804) hydrogen bonds : bond 0.04529 ( 428) hydrogen bonds : angle 4.80101 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 167 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7240 (ppp) cc_final: 0.6143 (ppp) REVERT: A 22 HIS cc_start: 0.7755 (t-90) cc_final: 0.7372 (t70) REVERT: A 74 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8120 (ttp-110) REVERT: A 191 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 210 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8577 (tp) REVERT: D 16 MET cc_start: 0.7449 (ppp) cc_final: 0.6431 (ppp) REVERT: D 22 HIS cc_start: 0.7768 (t-90) cc_final: 0.7367 (t70) REVERT: D 74 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8118 (ttp-110) REVERT: D 191 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7809 (tm-30) REVERT: E 16 MET cc_start: 0.7337 (ppp) cc_final: 0.7125 (ppp) REVERT: E 22 HIS cc_start: 0.7708 (t-90) cc_final: 0.7280 (t70) REVERT: E 191 GLU cc_start: 0.8544 (tm-30) cc_final: 0.7831 (tm-30) REVERT: F 16 MET cc_start: 0.7404 (ppp) cc_final: 0.6504 (ppp) REVERT: F 22 HIS cc_start: 0.7721 (t-90) cc_final: 0.7289 (t70) REVERT: F 74 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8089 (ttp-110) REVERT: F 191 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7784 (tm-30) REVERT: F 210 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8544 (tp) outliers start: 69 outliers final: 33 residues processed: 222 average time/residue: 0.0886 time to fit residues: 26.4503 Evaluate side-chains 202 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.0970 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 0.0170 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.139072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105393 restraints weight = 11829.837| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.87 r_work: 0.3235 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7988 Z= 0.107 Angle : 0.528 6.525 10804 Z= 0.271 Chirality : 0.039 0.193 1232 Planarity : 0.005 0.051 1256 Dihedral : 19.412 96.169 1362 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.72 % Favored : 93.83 % Rotamer: Outliers : 7.91 % Allowed : 18.97 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.28), residues: 892 helix: 0.59 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.67 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 199 TYR 0.006 0.001 TYR D 49 PHE 0.014 0.001 PHE F 215 TRP 0.003 0.000 TRP D 54 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7988) covalent geometry : angle 0.52801 (10804) hydrogen bonds : bond 0.03572 ( 428) hydrogen bonds : angle 4.11736 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7636 (t-90) cc_final: 0.7250 (t-170) REVERT: A 42 ILE cc_start: 0.9476 (tt) cc_final: 0.9250 (tt) REVERT: A 73 MET cc_start: 0.8723 (mtp) cc_final: 0.8519 (mtp) REVERT: A 74 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8047 (ttp-110) REVERT: A 90 ASN cc_start: 0.9024 (m-40) cc_final: 0.8704 (m110) REVERT: A 191 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8061 (tm-30) REVERT: D 16 MET cc_start: 0.6614 (ppp) cc_final: 0.6186 (ppp) REVERT: D 22 HIS cc_start: 0.7618 (t-90) cc_final: 0.7221 (t-170) REVERT: D 42 ILE cc_start: 0.9472 (tt) cc_final: 0.9249 (tt) REVERT: D 73 MET cc_start: 0.8883 (mtp) cc_final: 0.8678 (mtp) REVERT: D 131 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8492 (ttm170) REVERT: D 191 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8080 (tm-30) REVERT: E 22 HIS cc_start: 0.7637 (t-90) cc_final: 0.7209 (t-170) REVERT: E 42 ILE cc_start: 0.9469 (tt) cc_final: 0.9249 (tt) REVERT: E 73 MET cc_start: 0.8715 (mtp) cc_final: 0.8514 (mtp) REVERT: E 131 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8504 (ttm170) REVERT: E 191 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8062 (tm-30) REVERT: F 22 HIS cc_start: 0.7669 (t-90) cc_final: 0.7263 (t-170) REVERT: F 74 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8147 (ttp-110) REVERT: F 90 ASN cc_start: 0.9022 (m-40) cc_final: 0.8694 (m110) REVERT: F 102 ILE cc_start: 0.8603 (mt) cc_final: 0.8207 (pt) REVERT: F 131 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8445 (ttm-80) REVERT: F 191 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8044 (tm-30) outliers start: 63 outliers final: 43 residues processed: 225 average time/residue: 0.0811 time to fit residues: 25.4589 Evaluate side-chains 218 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 195 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 75 optimal weight: 0.0370 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.139582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105756 restraints weight = 12018.944| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.93 r_work: 0.3229 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7988 Z= 0.111 Angle : 0.587 12.433 10804 Z= 0.277 Chirality : 0.039 0.222 1232 Planarity : 0.008 0.116 1256 Dihedral : 18.514 90.438 1350 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.05 % Favored : 93.50 % Rotamer: Outliers : 7.16 % Allowed : 20.10 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.29), residues: 892 helix: 1.02 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.60 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 122 TYR 0.006 0.001 TYR F 156 PHE 0.020 0.001 PHE A 215 TRP 0.004 0.000 TRP D 54 HIS 0.001 0.000 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7988) covalent geometry : angle 0.58673 (10804) hydrogen bonds : bond 0.03443 ( 428) hydrogen bonds : angle 3.95510 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6868 (ppp) cc_final: 0.6129 (ppp) REVERT: A 22 HIS cc_start: 0.7607 (t-90) cc_final: 0.7230 (t-170) REVERT: A 42 ILE cc_start: 0.9488 (tt) cc_final: 0.9257 (tt) REVERT: A 74 ARG cc_start: 0.8614 (ttm-80) cc_final: 0.8404 (ttm-80) REVERT: A 90 ASN cc_start: 0.9075 (m-40) cc_final: 0.8745 (m110) REVERT: D 22 HIS cc_start: 0.7617 (t-90) cc_final: 0.7231 (t-170) REVERT: D 42 ILE cc_start: 0.9488 (tt) cc_final: 0.9254 (tt) REVERT: D 73 MET cc_start: 0.8856 (mtp) cc_final: 0.8646 (mtp) REVERT: E 22 HIS cc_start: 0.7690 (t-90) cc_final: 0.7260 (t-170) REVERT: E 42 ILE cc_start: 0.9492 (tt) cc_final: 0.9258 (tt) REVERT: F 16 MET cc_start: 0.6924 (ppp) cc_final: 0.6050 (ppp) REVERT: F 22 HIS cc_start: 0.7640 (t-90) cc_final: 0.7237 (t-170) REVERT: F 74 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8122 (ttp-110) REVERT: F 90 ASN cc_start: 0.9074 (m-40) cc_final: 0.8712 (m110) REVERT: F 102 ILE cc_start: 0.8556 (mt) cc_final: 0.8309 (pt) REVERT: F 191 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8051 (tm-30) outliers start: 57 outliers final: 42 residues processed: 214 average time/residue: 0.0723 time to fit residues: 22.0414 Evaluate side-chains 211 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.139364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105309 restraints weight = 11921.466| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.93 r_work: 0.3207 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7988 Z= 0.132 Angle : 0.574 14.796 10804 Z= 0.285 Chirality : 0.041 0.239 1232 Planarity : 0.004 0.038 1256 Dihedral : 18.162 88.449 1350 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 7.91 % Allowed : 19.60 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.29 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.29), residues: 892 helix: 1.22 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 122 TYR 0.007 0.001 TYR A 211 PHE 0.022 0.001 PHE D 215 TRP 0.003 0.000 TRP A 54 HIS 0.000 0.000 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7988) covalent geometry : angle 0.57415 (10804) hydrogen bonds : bond 0.03523 ( 428) hydrogen bonds : angle 4.02794 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6970 (ppp) cc_final: 0.6373 (ppp) REVERT: A 22 HIS cc_start: 0.7545 (t-90) cc_final: 0.7208 (t-170) REVERT: A 42 ILE cc_start: 0.9489 (tt) cc_final: 0.9269 (tt) REVERT: A 90 ASN cc_start: 0.9118 (m-40) cc_final: 0.8873 (m-40) REVERT: A 191 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 210 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8472 (tp) REVERT: D 22 HIS cc_start: 0.7732 (t-90) cc_final: 0.7323 (t-170) REVERT: D 42 ILE cc_start: 0.9460 (tt) cc_final: 0.9213 (tt) REVERT: D 73 MET cc_start: 0.8833 (mtp) cc_final: 0.8580 (mtp) REVERT: D 191 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8182 (tm-30) REVERT: E 22 HIS cc_start: 0.7633 (t-90) cc_final: 0.7196 (t-170) REVERT: E 42 ILE cc_start: 0.9491 (tt) cc_final: 0.9252 (tt) REVERT: E 73 MET cc_start: 0.8537 (mtp) cc_final: 0.8329 (mtp) REVERT: E 191 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8180 (tm-30) REVERT: F 16 MET cc_start: 0.6962 (ppp) cc_final: 0.6335 (ppp) REVERT: F 22 HIS cc_start: 0.7578 (t-90) cc_final: 0.7207 (t-170) REVERT: F 102 ILE cc_start: 0.8577 (mt) cc_final: 0.8370 (pt) REVERT: F 191 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8151 (tm-30) REVERT: F 210 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8472 (tp) outliers start: 63 outliers final: 45 residues processed: 225 average time/residue: 0.0671 time to fit residues: 22.0031 Evaluate side-chains 220 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.137731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103914 restraints weight = 11900.818| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.87 r_work: 0.3205 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7988 Z= 0.138 Angle : 0.607 13.959 10804 Z= 0.292 Chirality : 0.041 0.198 1232 Planarity : 0.004 0.037 1256 Dihedral : 17.911 88.794 1346 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.29 % Allowed : 20.35 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.29), residues: 892 helix: 1.28 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.90 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 74 TYR 0.008 0.001 TYR D 211 PHE 0.021 0.001 PHE F 215 TRP 0.003 0.001 TRP D 209 HIS 0.001 0.000 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7988) covalent geometry : angle 0.60664 (10804) hydrogen bonds : bond 0.03528 ( 428) hydrogen bonds : angle 4.08008 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6825 (ppp) cc_final: 0.6386 (ppp) REVERT: A 22 HIS cc_start: 0.7546 (t-90) cc_final: 0.7198 (t-170) REVERT: A 191 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 220 THR cc_start: 0.9371 (m) cc_final: 0.9024 (m) REVERT: D 22 HIS cc_start: 0.7646 (t-90) cc_final: 0.7272 (t-170) REVERT: D 73 MET cc_start: 0.8793 (mtp) cc_final: 0.8522 (mtp) REVERT: D 90 ASN cc_start: 0.9191 (m-40) cc_final: 0.8960 (m-40) REVERT: D 191 GLU cc_start: 0.8609 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 220 THR cc_start: 0.9337 (m) cc_final: 0.8951 (m) REVERT: E 22 HIS cc_start: 0.7553 (t-90) cc_final: 0.7155 (t-170) REVERT: E 191 GLU cc_start: 0.8646 (tm-30) cc_final: 0.7864 (tm-30) REVERT: E 220 THR cc_start: 0.9383 (m) cc_final: 0.9037 (m) REVERT: F 16 MET cc_start: 0.6905 (ppp) cc_final: 0.6437 (ppp) REVERT: F 22 HIS cc_start: 0.7568 (t-90) cc_final: 0.7195 (t-170) REVERT: F 191 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7732 (tm-30) REVERT: F 220 THR cc_start: 0.9365 (m) cc_final: 0.9020 (m) outliers start: 58 outliers final: 49 residues processed: 212 average time/residue: 0.0580 time to fit residues: 18.8641 Evaluate side-chains 224 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 195 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.0270 chunk 81 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.139281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105740 restraints weight = 11858.971| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.86 r_work: 0.3241 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7988 Z= 0.113 Angle : 0.559 7.293 10804 Z= 0.277 Chirality : 0.041 0.229 1232 Planarity : 0.004 0.036 1256 Dihedral : 17.514 89.964 1346 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 6.53 % Allowed : 19.97 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.29), residues: 892 helix: 1.45 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.92 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 74 TYR 0.007 0.001 TYR A 211 PHE 0.019 0.001 PHE F 215 TRP 0.002 0.000 TRP A 193 HIS 0.002 0.000 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7988) covalent geometry : angle 0.55900 (10804) hydrogen bonds : bond 0.03296 ( 428) hydrogen bonds : angle 3.98961 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.220 Fit side-chains REVERT: A 16 MET cc_start: 0.6770 (ppp) cc_final: 0.6433 (ppp) REVERT: A 22 HIS cc_start: 0.7476 (t-90) cc_final: 0.7174 (t-170) REVERT: A 43 GLU cc_start: 0.8729 (pt0) cc_final: 0.8487 (pt0) REVERT: A 90 ASN cc_start: 0.9104 (m-40) cc_final: 0.8781 (m110) REVERT: A 191 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 210 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8410 (tp) REVERT: A 220 THR cc_start: 0.9342 (m) cc_final: 0.9007 (m) REVERT: D 22 HIS cc_start: 0.7505 (t-90) cc_final: 0.7195 (t-170) REVERT: D 73 MET cc_start: 0.8740 (mtp) cc_final: 0.8466 (mtp) REVERT: D 90 ASN cc_start: 0.9177 (m-40) cc_final: 0.8956 (m-40) REVERT: D 191 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8137 (tm-30) REVERT: D 220 THR cc_start: 0.9330 (m) cc_final: 0.8966 (m) REVERT: E 22 HIS cc_start: 0.7502 (t-90) cc_final: 0.7140 (t-170) REVERT: E 191 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8115 (tm-30) REVERT: E 220 THR cc_start: 0.9355 (m) cc_final: 0.9023 (m) REVERT: F 16 MET cc_start: 0.6683 (ppp) cc_final: 0.6393 (ppp) REVERT: F 22 HIS cc_start: 0.7515 (t-90) cc_final: 0.7185 (t-170) REVERT: F 90 ASN cc_start: 0.9134 (m-40) cc_final: 0.8886 (m110) REVERT: F 191 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8126 (tm-30) REVERT: F 210 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8418 (tp) REVERT: F 220 THR cc_start: 0.9342 (m) cc_final: 0.9007 (m) outliers start: 52 outliers final: 43 residues processed: 222 average time/residue: 0.0694 time to fit residues: 22.1583 Evaluate side-chains 231 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.0570 chunk 19 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.140453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106962 restraints weight = 11937.686| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.87 r_work: 0.3260 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7988 Z= 0.113 Angle : 0.615 13.424 10804 Z= 0.291 Chirality : 0.042 0.222 1232 Planarity : 0.004 0.036 1256 Dihedral : 17.113 89.144 1341 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.53 % Allowed : 20.85 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.29), residues: 892 helix: 1.52 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.90 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 74 TYR 0.007 0.001 TYR D 211 PHE 0.019 0.001 PHE F 215 TRP 0.008 0.001 TRP F 65 HIS 0.000 0.000 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7988) covalent geometry : angle 0.61532 (10804) hydrogen bonds : bond 0.03314 ( 428) hydrogen bonds : angle 3.99132 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.293 Fit side-chains REVERT: A 16 MET cc_start: 0.6606 (ppp) cc_final: 0.6375 (ppp) REVERT: A 22 HIS cc_start: 0.7343 (t-90) cc_final: 0.7075 (t-170) REVERT: A 90 ASN cc_start: 0.9108 (m-40) cc_final: 0.8808 (m110) REVERT: A 191 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 210 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8364 (tp) REVERT: A 220 THR cc_start: 0.9328 (m) cc_final: 0.9006 (m) REVERT: D 22 HIS cc_start: 0.7459 (t-90) cc_final: 0.7170 (t-170) REVERT: D 90 ASN cc_start: 0.9177 (m-40) cc_final: 0.8961 (m110) REVERT: D 220 THR cc_start: 0.9309 (m) cc_final: 0.8977 (m) REVERT: E 22 HIS cc_start: 0.7455 (t-90) cc_final: 0.7112 (t-170) REVERT: E 220 THR cc_start: 0.9335 (m) cc_final: 0.9013 (m) REVERT: F 16 MET cc_start: 0.6637 (ppp) cc_final: 0.6403 (ppp) REVERT: F 22 HIS cc_start: 0.7504 (t-90) cc_final: 0.7244 (t-170) REVERT: F 90 ASN cc_start: 0.9125 (m-40) cc_final: 0.8904 (m110) REVERT: F 191 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8057 (tm-30) REVERT: F 210 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8362 (tp) REVERT: F 220 THR cc_start: 0.9281 (m) cc_final: 0.8949 (m) outliers start: 52 outliers final: 40 residues processed: 217 average time/residue: 0.0576 time to fit residues: 19.0900 Evaluate side-chains 217 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.139049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105628 restraints weight = 11871.228| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.86 r_work: 0.3235 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7988 Z= 0.131 Angle : 0.618 12.632 10804 Z= 0.297 Chirality : 0.042 0.201 1232 Planarity : 0.004 0.035 1256 Dihedral : 16.815 87.896 1332 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.28 % Allowed : 21.23 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.29), residues: 892 helix: 1.54 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.88 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.008 0.001 TYR D 211 PHE 0.019 0.001 PHE F 215 TRP 0.004 0.001 TRP E 89 HIS 0.000 0.000 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7988) covalent geometry : angle 0.61790 (10804) hydrogen bonds : bond 0.03447 ( 428) hydrogen bonds : angle 4.08539 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7356 (t-90) cc_final: 0.7071 (t-170) REVERT: A 90 ASN cc_start: 0.9110 (m-40) cc_final: 0.8823 (m110) REVERT: A 191 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8176 (tm-30) REVERT: A 210 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8463 (tp) REVERT: A 220 THR cc_start: 0.9278 (m) cc_final: 0.8947 (m) REVERT: D 22 HIS cc_start: 0.7462 (t-90) cc_final: 0.7151 (t-170) REVERT: D 36 ASN cc_start: 0.9291 (t0) cc_final: 0.8847 (t0) REVERT: D 73 MET cc_start: 0.8867 (mtm) cc_final: 0.8577 (mtp) REVERT: D 191 GLU cc_start: 0.8609 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 220 THR cc_start: 0.9319 (m) cc_final: 0.8977 (m) REVERT: E 22 HIS cc_start: 0.7460 (t-90) cc_final: 0.7109 (t-170) REVERT: E 36 ASN cc_start: 0.9297 (t0) cc_final: 0.9019 (t0) REVERT: E 191 GLU cc_start: 0.8633 (tm-30) cc_final: 0.7841 (tm-30) REVERT: E 220 THR cc_start: 0.9341 (m) cc_final: 0.9015 (m) REVERT: F 22 HIS cc_start: 0.7514 (t-90) cc_final: 0.7180 (t-170) REVERT: F 191 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8100 (tm-30) REVERT: F 210 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8447 (tp) REVERT: F 220 THR cc_start: 0.9282 (m) cc_final: 0.8950 (m) outliers start: 50 outliers final: 44 residues processed: 213 average time/residue: 0.0585 time to fit residues: 18.9253 Evaluate side-chains 224 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.139152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.104116 restraints weight = 12023.891| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.09 r_work: 0.3199 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7988 Z= 0.126 Angle : 0.687 19.482 10804 Z= 0.318 Chirality : 0.042 0.198 1232 Planarity : 0.004 0.035 1256 Dihedral : 16.738 87.140 1332 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.28 % Allowed : 21.11 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.30), residues: 892 helix: 1.59 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 74 TYR 0.007 0.001 TYR D 211 PHE 0.019 0.001 PHE F 215 TRP 0.003 0.000 TRP E 89 HIS 0.000 0.000 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7988) covalent geometry : angle 0.68749 (10804) hydrogen bonds : bond 0.03373 ( 428) hydrogen bonds : angle 4.04607 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7405 (t-90) cc_final: 0.7145 (t-170) REVERT: A 36 ASN cc_start: 0.9164 (t0) cc_final: 0.8702 (t0) REVERT: A 90 ASN cc_start: 0.9029 (m-40) cc_final: 0.8749 (m110) REVERT: A 191 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 210 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8293 (tp) REVERT: A 220 THR cc_start: 0.9176 (m) cc_final: 0.8830 (m) REVERT: D 22 HIS cc_start: 0.7329 (t-90) cc_final: 0.7088 (t-170) REVERT: D 36 ASN cc_start: 0.9232 (t0) cc_final: 0.8712 (t0) REVERT: D 73 MET cc_start: 0.8780 (mtm) cc_final: 0.8468 (mtp) REVERT: D 191 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8043 (tm-30) REVERT: D 220 THR cc_start: 0.9223 (m) cc_final: 0.8882 (m) REVERT: E 22 HIS cc_start: 0.7329 (t-90) cc_final: 0.7037 (t-170) REVERT: E 36 ASN cc_start: 0.9225 (t0) cc_final: 0.8889 (t0) REVERT: E 191 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8039 (tm-30) REVERT: E 220 THR cc_start: 0.9233 (m) cc_final: 0.8907 (m) REVERT: F 22 HIS cc_start: 0.7475 (t-90) cc_final: 0.7187 (t-170) REVERT: F 191 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7985 (tm-30) REVERT: F 210 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8274 (tp) REVERT: F 220 THR cc_start: 0.9188 (m) cc_final: 0.8852 (m) outliers start: 50 outliers final: 46 residues processed: 215 average time/residue: 0.0603 time to fit residues: 19.7479 Evaluate side-chains 229 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 226 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.140181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106235 restraints weight = 11798.798| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.91 r_work: 0.3231 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7988 Z= 0.132 Angle : 0.638 14.166 10804 Z= 0.303 Chirality : 0.042 0.197 1232 Planarity : 0.004 0.036 1256 Dihedral : 16.769 86.474 1332 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 6.41 % Allowed : 20.85 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.30), residues: 892 helix: 1.58 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.68 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 74 TYR 0.008 0.001 TYR D 211 PHE 0.019 0.001 PHE F 215 TRP 0.004 0.001 TRP E 89 HIS 0.000 0.000 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7988) covalent geometry : angle 0.63777 (10804) hydrogen bonds : bond 0.03454 ( 428) hydrogen bonds : angle 4.07133 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.03 seconds wall clock time: 38 minutes 55.78 seconds (2335.78 seconds total)