Starting phenix.real_space_refine on Wed Feb 12 15:04:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwx_21425/02_2025/6vwx_21425_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwx_21425/02_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_21425/02_2025/6vwx_21425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwx_21425/02_2025/6vwx_21425.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwx_21425/02_2025/6vwx_21425_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwx_21425/02_2025/6vwx_21425_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.43, per 1000 atoms: 0.70 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: 2.04 Conformation dependent library (CDL) restraints added in 958.9 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: 0.63 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: 1.97 Time building geometry restraints manager: 2.31 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 237 or resid 301 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: 0.900 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.580 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- 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= 0.675 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP A 91 HIS 0.001 0.000 HIS F 22 PHE 0.012 0.001 PHE D 174 TYR 0.007 0.001 TYR D 156 ARG 0.002 0.000 ARG F 116 *********************** 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 : 0.892 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: 0.1783 time to fit residues: 65.0087 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 : 0.914 ------------------------------------------------------------------------------- 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 74 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.137162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102893 restraints weight = 11694.959| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.96 r_work: 0.3174 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7988 Z= 0.210 Angle : 0.607 10.577 10804 Z= 0.313 Chirality : 0.040 0.191 1232 Planarity : 0.006 0.055 1256 Dihedral : 21.478 107.539 1477 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.17 % Favored : 92.38 % Rotamer: Outliers : 8.42 % Allowed : 18.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.27), residues: 892 helix: -0.26 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 54 HIS 0.001 0.000 HIS F 22 PHE 0.015 0.001 PHE F 215 TYR 0.006 0.001 TYR D 156 ARG 0.003 0.000 ARG A 131 *********************** 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 239 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7246 (ppp) cc_final: 0.6255 (ppp) REVERT: A 22 HIS cc_start: 0.7739 (t-90) cc_final: 0.7375 (t70) REVERT: A 74 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8103 (ttp-110) REVERT: A 90 ASN cc_start: 0.8983 (m-40) cc_final: 0.8698 (m110) REVERT: A 191 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7733 (tm-30) REVERT: D 16 MET cc_start: 0.7452 (ppp) cc_final: 0.6441 (ppp) REVERT: D 22 HIS cc_start: 0.7753 (t-90) cc_final: 0.7360 (t70) REVERT: D 74 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8114 (ttp-110) REVERT: D 191 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7730 (tm-30) REVERT: E 16 MET cc_start: 0.7237 (ppp) cc_final: 0.6944 (ppp) REVERT: E 22 HIS cc_start: 0.7718 (t-90) cc_final: 0.7298 (t70) REVERT: E 70 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: E 93 ASP cc_start: 0.8717 (m-30) cc_final: 0.8477 (m-30) REVERT: E 191 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7775 (tm-30) REVERT: F 16 MET cc_start: 0.7242 (ppp) cc_final: 0.6378 (ppp) REVERT: F 22 HIS cc_start: 0.7703 (t-90) cc_final: 0.7292 (t70) REVERT: F 74 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8112 (ttp-110) REVERT: F 90 ASN cc_start: 0.8968 (m-40) cc_final: 0.8687 (m110) REVERT: F 191 GLU cc_start: 0.8521 (tm-30) cc_final: 0.7738 (tm-30) outliers start: 67 outliers final: 28 residues processed: 225 average time/residue: 0.2017 time to fit residues: 60.5831 Evaluate side-chains 194 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 63 LEU Chi-restraints excluded: chain E residue 70 GLU 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.0570 chunk 87 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.139342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104723 restraints weight = 11959.658| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.97 r_work: 0.3209 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7988 Z= 0.186 Angle : 0.532 6.465 10804 Z= 0.275 Chirality : 0.039 0.192 1232 Planarity : 0.005 0.051 1256 Dihedral : 19.410 96.694 1355 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.83 % Favored : 93.72 % Rotamer: Outliers : 8.29 % Allowed : 18.34 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 892 helix: 0.60 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.66 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 54 HIS 0.001 0.000 HIS A 101 PHE 0.016 0.001 PHE E 215 TYR 0.006 0.001 TYR D 49 ARG 0.001 0.000 ARG F 122 *********************** 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: 66 poor density : 182 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6552 (ppp) cc_final: 0.6241 (ppp) REVERT: A 22 HIS cc_start: 0.7469 (t-90) cc_final: 0.7155 (t-170) REVERT: A 73 MET cc_start: 0.8682 (mtp) cc_final: 0.8476 (mtp) REVERT: A 74 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8014 (ttp-110) REVERT: A 90 ASN cc_start: 0.9002 (m-40) cc_final: 0.8670 (m110) REVERT: A 131 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8452 (ttm170) REVERT: A 191 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 210 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8433 (tp) REVERT: D 16 MET cc_start: 0.6603 (ppp) cc_final: 0.6201 (ppp) REVERT: D 22 HIS cc_start: 0.7477 (t-90) cc_final: 0.7152 (t-170) REVERT: D 131 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8449 (ttm170) REVERT: D 191 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7993 (tm-30) REVERT: E 22 HIS cc_start: 0.7485 (t-90) cc_final: 0.7129 (t-170) REVERT: E 73 MET cc_start: 0.8685 (mtp) cc_final: 0.8473 (mtp) REVERT: E 102 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8193 (pt) REVERT: E 191 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7634 (tm-30) REVERT: F 16 MET cc_start: 0.6626 (ppp) cc_final: 0.6262 (ppp) REVERT: F 22 HIS cc_start: 0.7519 (t-90) cc_final: 0.7171 (t-170) REVERT: F 74 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.7953 (ttp-110) REVERT: F 90 ASN cc_start: 0.9012 (m-40) cc_final: 0.8673 (m110) REVERT: F 102 ILE cc_start: 0.8584 (mt) cc_final: 0.8207 (pt) REVERT: F 191 GLU cc_start: 0.8459 (tm-30) cc_final: 0.7996 (tm-30) REVERT: F 210 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8451 (tp) outliers start: 66 outliers final: 46 residues processed: 225 average time/residue: 0.1890 time to fit residues: 57.7976 Evaluate side-chains 219 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 131 ARG 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 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 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 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 102 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 E residue 195 SER Chi-restraints excluded: chain F residue 48 ILE 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 Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.0170 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.138927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105175 restraints weight = 11895.508| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.92 r_work: 0.3220 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7988 Z= 0.166 Angle : 0.568 12.379 10804 Z= 0.273 Chirality : 0.040 0.220 1232 Planarity : 0.008 0.117 1256 Dihedral : 18.558 91.886 1348 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.83 % Favored : 93.72 % Rotamer: Outliers : 7.04 % Allowed : 19.72 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.29), residues: 892 helix: 0.97 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.54 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 54 HIS 0.001 0.000 HIS E 22 PHE 0.021 0.001 PHE A 215 TYR 0.006 0.001 TYR D 211 ARG 0.003 0.000 ARG A 122 *********************** 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 240 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7566 (t-90) cc_final: 0.7204 (t-170) REVERT: A 90 ASN cc_start: 0.9086 (m-40) cc_final: 0.8746 (m110) REVERT: A 131 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8500 (ttm170) REVERT: A 191 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 210 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8460 (tp) REVERT: D 22 HIS cc_start: 0.7627 (t-90) cc_final: 0.7228 (t-170) REVERT: D 131 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8498 (ttm170) REVERT: D 191 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 22 HIS cc_start: 0.7704 (t-90) cc_final: 0.7259 (t-170) REVERT: E 90 ASN cc_start: 0.9077 (m-40) cc_final: 0.8840 (m-40) REVERT: E 102 ILE cc_start: 0.8620 (mt) cc_final: 0.8325 (pt) REVERT: E 191 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8110 (tm-30) REVERT: F 22 HIS cc_start: 0.7608 (t-90) cc_final: 0.7215 (t-170) REVERT: F 73 MET cc_start: 0.8900 (mtp) cc_final: 0.8620 (mtp) REVERT: F 74 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8407 (ttm-80) REVERT: F 90 ASN cc_start: 0.9043 (m-40) cc_final: 0.8726 (m110) REVERT: F 102 ILE cc_start: 0.8558 (mt) cc_final: 0.8309 (pt) REVERT: F 191 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 210 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8463 (tp) outliers start: 56 outliers final: 37 residues processed: 219 average time/residue: 0.1630 time to fit residues: 50.4291 Evaluate side-chains 222 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 ARG 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 210 LEU Chi-restraints excluded: chain A residue 226 LEU 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 195 SER 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 178 GLN Chi-restraints excluded: chain E residue 195 SER 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 210 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 0.0040 chunk 2 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.138937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105081 restraints weight = 11751.687| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.87 r_work: 0.3221 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7988 Z= 0.185 Angle : 0.632 14.770 10804 Z= 0.301 Chirality : 0.041 0.254 1232 Planarity : 0.004 0.037 1256 Dihedral : 18.094 89.265 1344 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.91 % Allowed : 19.47 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.29), residues: 892 helix: 1.23 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.68 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 54 HIS 0.001 0.000 HIS F 22 PHE 0.022 0.001 PHE D 215 TYR 0.007 0.001 TYR A 211 ARG 0.005 0.000 ARG A 74 *********************** 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 236 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7596 (t-90) cc_final: 0.7249 (t-170) REVERT: A 90 ASN cc_start: 0.9124 (m-40) cc_final: 0.8869 (m-40) REVERT: A 131 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8520 (ttm170) REVERT: A 191 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8151 (tm-30) REVERT: A 210 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8493 (tp) REVERT: D 22 HIS cc_start: 0.7712 (t-90) cc_final: 0.7313 (t-170) REVERT: D 131 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8515 (ttm170) REVERT: D 191 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8154 (tm-30) REVERT: E 22 HIS cc_start: 0.7616 (t-90) cc_final: 0.7187 (t-170) REVERT: E 73 MET cc_start: 0.8533 (mtp) cc_final: 0.8325 (mtp) REVERT: E 102 ILE cc_start: 0.8526 (mt) cc_final: 0.8321 (pt) REVERT: E 191 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8131 (tm-30) REVERT: F 22 HIS cc_start: 0.7628 (t-90) cc_final: 0.7257 (t-170) REVERT: F 73 MET cc_start: 0.8885 (mtp) cc_final: 0.8574 (mtp) REVERT: F 191 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8070 (tm-30) REVERT: F 210 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8470 (tp) outliers start: 55 outliers final: 43 residues processed: 218 average time/residue: 0.1629 time to fit residues: 50.2186 Evaluate side-chains 221 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 131 ARG 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 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 195 SER 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 E residue 195 SER Chi-restraints excluded: chain E residue 235 VAL 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 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 76 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.138923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105390 restraints weight = 11832.769| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.86 r_work: 0.3228 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7988 Z= 0.174 Angle : 0.580 13.843 10804 Z= 0.287 Chirality : 0.041 0.241 1232 Planarity : 0.004 0.036 1256 Dihedral : 17.746 88.668 1344 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.91 % Allowed : 21.36 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 892 helix: 1.33 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.85 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 193 HIS 0.001 0.000 HIS D 101 PHE 0.021 0.001 PHE F 215 TYR 0.007 0.001 TYR E 211 ARG 0.004 0.000 ARG F 74 *********************** 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 234 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7507 (t-90) cc_final: 0.7194 (t-170) REVERT: A 131 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8511 (ttm170) REVERT: A 191 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 210 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8462 (tp) REVERT: A 220 THR cc_start: 0.9363 (m) cc_final: 0.9013 (m) REVERT: D 22 HIS cc_start: 0.7569 (t-90) cc_final: 0.7228 (t-170) REVERT: D 90 ASN cc_start: 0.9183 (m-40) cc_final: 0.8963 (m-40) REVERT: D 131 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8524 (ttm170) REVERT: D 191 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8166 (tm-30) REVERT: D 220 THR cc_start: 0.9340 (m) cc_final: 0.8969 (m) REVERT: E 22 HIS cc_start: 0.7543 (t-90) cc_final: 0.7145 (t-170) REVERT: E 191 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8118 (tm-30) REVERT: E 220 THR cc_start: 0.9356 (m) cc_final: 0.9017 (m) REVERT: F 22 HIS cc_start: 0.7559 (t-90) cc_final: 0.7209 (t-170) REVERT: F 73 MET cc_start: 0.8814 (mtp) cc_final: 0.8485 (mtp) REVERT: F 90 ASN cc_start: 0.9125 (m-40) cc_final: 0.8884 (m-40) REVERT: F 191 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8066 (tm-30) REVERT: F 210 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8455 (tp) REVERT: F 220 THR cc_start: 0.9338 (m) cc_final: 0.8990 (m) outliers start: 55 outliers final: 43 residues processed: 211 average time/residue: 0.1673 time to fit residues: 49.6139 Evaluate side-chains 219 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 131 ARG 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 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 E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP 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 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 34 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 10 optimal weight: 0.1980 chunk 87 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.140102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106865 restraints weight = 11773.408| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.84 r_work: 0.3257 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7988 Z= 0.155 Angle : 0.571 8.572 10804 Z= 0.286 Chirality : 0.041 0.269 1232 Planarity : 0.004 0.036 1256 Dihedral : 17.439 89.708 1344 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 6.41 % Allowed : 20.73 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.29), residues: 892 helix: 1.48 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.86 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 65 HIS 0.001 0.000 HIS F 101 PHE 0.019 0.001 PHE F 215 TYR 0.007 0.001 TYR D 211 ARG 0.004 0.000 ARG F 74 *********************** 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 234 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.811 Fit side-chains REVERT: A 22 HIS cc_start: 0.7533 (t-90) cc_final: 0.7228 (t-170) REVERT: A 90 ASN cc_start: 0.9175 (m-40) cc_final: 0.8930 (m110) REVERT: A 131 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8516 (ttm170) REVERT: A 191 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 220 THR cc_start: 0.9327 (m) cc_final: 0.8982 (m) REVERT: D 22 HIS cc_start: 0.7469 (t-90) cc_final: 0.7161 (t-170) REVERT: D 90 ASN cc_start: 0.9171 (m-40) cc_final: 0.8959 (m-40) REVERT: D 131 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8564 (ttm170) REVERT: D 191 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8089 (tm-30) REVERT: D 220 THR cc_start: 0.9324 (m) cc_final: 0.8973 (m) REVERT: E 22 HIS cc_start: 0.7518 (t-90) cc_final: 0.7151 (t-170) REVERT: E 90 ASN cc_start: 0.9141 (m-40) cc_final: 0.8928 (m-40) REVERT: E 191 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8064 (tm-30) REVERT: E 220 THR cc_start: 0.9307 (m) cc_final: 0.8972 (m) REVERT: F 22 HIS cc_start: 0.7511 (t-90) cc_final: 0.7196 (t-170) REVERT: F 73 MET cc_start: 0.8805 (mtp) cc_final: 0.8447 (mtp) REVERT: F 90 ASN cc_start: 0.9141 (m-40) cc_final: 0.8900 (m110) REVERT: F 191 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8062 (tm-30) REVERT: F 220 THR cc_start: 0.9307 (m) cc_final: 0.8963 (m) outliers start: 51 outliers final: 45 residues processed: 211 average time/residue: 0.1547 time to fit residues: 47.6517 Evaluate side-chains 226 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 63 LEU 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 131 ARG 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 34 LEU 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 E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 70 GLU 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 E residue 195 SER 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 178 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 226 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 53 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.138681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105287 restraints weight = 11837.742| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.85 r_work: 0.3233 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3291 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= 0.191 Angle : 0.604 12.876 10804 Z= 0.297 Chirality : 0.042 0.226 1232 Planarity : 0.004 0.035 1256 Dihedral : 17.393 89.156 1344 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.91 % Allowed : 20.85 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 892 helix: 1.52 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.87 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 209 HIS 0.001 0.000 HIS E 101 PHE 0.020 0.001 PHE F 215 TYR 0.015 0.001 TYR A 49 ARG 0.004 0.000 ARG F 74 *********************** 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 240 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7522 (t-90) cc_final: 0.7213 (t-170) REVERT: A 131 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8518 (ttm170) REVERT: A 191 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 210 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8470 (tp) REVERT: A 220 THR cc_start: 0.9302 (m) cc_final: 0.8963 (m) REVERT: D 22 HIS cc_start: 0.7468 (t-90) cc_final: 0.7162 (t-170) REVERT: D 131 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8533 (ttm170) REVERT: D 191 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 220 THR cc_start: 0.9328 (m) cc_final: 0.8983 (m) REVERT: E 22 HIS cc_start: 0.7490 (t-90) cc_final: 0.7133 (t-170) REVERT: E 191 GLU cc_start: 0.8629 (tm-30) cc_final: 0.7832 (tm-30) REVERT: E 220 THR cc_start: 0.9288 (m) cc_final: 0.8956 (m) REVERT: F 22 HIS cc_start: 0.7489 (t-90) cc_final: 0.7177 (t-170) REVERT: F 191 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8112 (tm-30) REVERT: F 210 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8462 (tp) REVERT: F 220 THR cc_start: 0.9310 (m) cc_final: 0.8968 (m) outliers start: 55 outliers final: 47 residues processed: 215 average time/residue: 0.1464 time to fit residues: 45.6622 Evaluate side-chains 231 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 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 131 ARG 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 34 LEU 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 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 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 70 GLU 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 195 SER 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 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 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 17 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.140546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106388 restraints weight = 11972.133| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.94 r_work: 0.3230 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3359 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= 0.175 Angle : 0.603 12.806 10804 Z= 0.295 Chirality : 0.041 0.230 1232 Planarity : 0.004 0.035 1256 Dihedral : 16.899 88.330 1335 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.53 % Allowed : 21.36 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.30), residues: 892 helix: 1.53 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.82 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 193 HIS 0.001 0.000 HIS E 101 PHE 0.019 0.001 PHE F 215 TYR 0.007 0.001 TYR E 211 ARG 0.003 0.000 ARG F 74 *********************** 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: 52 poor density : 181 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7274 (t-90) cc_final: 0.7056 (t-170) REVERT: A 131 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8443 (ttm170) REVERT: A 191 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 210 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8341 (tp) REVERT: A 220 THR cc_start: 0.9204 (m) cc_final: 0.8851 (m) REVERT: D 22 HIS cc_start: 0.7287 (t-90) cc_final: 0.7062 (t-170) REVERT: D 131 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8512 (ttm170) REVERT: D 191 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8042 (tm-30) REVERT: D 220 THR cc_start: 0.9244 (m) cc_final: 0.8894 (m) REVERT: E 22 HIS cc_start: 0.7328 (t-90) cc_final: 0.7054 (t-170) REVERT: E 191 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7649 (tm-30) REVERT: E 220 THR cc_start: 0.9217 (m) cc_final: 0.8892 (m) REVERT: F 22 HIS cc_start: 0.7274 (t-90) cc_final: 0.7055 (t-170) REVERT: F 191 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7947 (tm-30) REVERT: F 210 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8332 (tp) REVERT: F 220 THR cc_start: 0.9206 (m) cc_final: 0.8868 (m) outliers start: 52 outliers final: 46 residues processed: 212 average time/residue: 0.1509 time to fit residues: 46.3692 Evaluate side-chains 229 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 131 ARG 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 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 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 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 70 GLU 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 195 SER 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 65 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.138756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105328 restraints weight = 11902.914| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.85 r_work: 0.3238 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3434 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= 0.195 Angle : 0.610 12.540 10804 Z= 0.300 Chirality : 0.041 0.198 1232 Planarity : 0.004 0.035 1256 Dihedral : 16.830 87.472 1332 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 7.04 % Allowed : 21.23 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.30), residues: 892 helix: 1.53 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.69 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 89 HIS 0.001 0.000 HIS F 101 PHE 0.020 0.001 PHE F 215 TYR 0.008 0.001 TYR E 211 ARG 0.003 0.000 ARG F 74 ********************** 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 234 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7415 (t-90) cc_final: 0.7112 (t-170) REVERT: A 131 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8519 (ttm170) REVERT: A 191 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 210 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8506 (tp) REVERT: A 220 THR cc_start: 0.9274 (m) cc_final: 0.8940 (m) REVERT: D 22 HIS cc_start: 0.7384 (t-90) cc_final: 0.7113 (t-170) REVERT: D 131 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8589 (ttm170) REVERT: D 191 GLU cc_start: 0.8614 (tm-30) cc_final: 0.7800 (tm-30) REVERT: D 220 THR cc_start: 0.9317 (m) cc_final: 0.8974 (m) REVERT: E 22 HIS cc_start: 0.7446 (t-90) cc_final: 0.7116 (t-170) REVERT: E 135 ASP cc_start: 0.8574 (t0) cc_final: 0.8370 (t0) REVERT: E 191 GLU cc_start: 0.8647 (tm-30) cc_final: 0.7854 (tm-30) REVERT: E 220 THR cc_start: 0.9282 (m) cc_final: 0.8965 (m) REVERT: F 22 HIS cc_start: 0.7456 (t-90) cc_final: 0.7153 (t-170) REVERT: F 191 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8109 (tm-30) REVERT: F 210 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8536 (tp) REVERT: F 220 THR cc_start: 0.9277 (m) cc_final: 0.8934 (m) outliers start: 56 outliers final: 48 residues processed: 210 average time/residue: 0.1469 time to fit residues: 44.9333 Evaluate side-chains 231 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 131 ARG 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 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 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 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP 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 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 195 SER 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 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 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 21 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 81 optimal weight: 0.2980 chunk 63 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.141416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.108321 restraints weight = 11803.522| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.84 r_work: 0.3307 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7988 Z= 0.146 Angle : 0.597 13.161 10804 Z= 0.288 Chirality : 0.040 0.185 1232 Planarity : 0.004 0.034 1256 Dihedral : 16.500 86.027 1332 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.90 % Allowed : 22.24 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.30), residues: 892 helix: 1.51 (0.21), residues: 700 sheet: None (None), residues: 0 loop : -2.35 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 65 HIS 0.001 0.000 HIS A 52 PHE 0.017 0.001 PHE D 215 TYR 0.007 0.001 TYR D 211 ARG 0.003 0.000 ARG F 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3986.01 seconds wall clock time: 71 minutes 24.33 seconds (4284.33 seconds total)