Starting phenix.real_space_refine on Tue Mar 3 18:34:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwx_21425/03_2026/6vwx_21425_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwx_21425/03_2026/6vwx_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vwx_21425/03_2026/6vwx_21425_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwx_21425/03_2026/6vwx_21425_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vwx_21425/03_2026/6vwx_21425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwx_21425/03_2026/6vwx_21425.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 24 5.16 5 Na 2 4.78 5 C 5336 2.51 5 N 1188 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7782 Number of models: 1 Model: "" Number of chains: 8 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: "D" 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: "F" 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: "D" 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} 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} Chain: "F" 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} Time building chain proxies: 1.89, per 1000 atoms: 0.24 Number of scatterers: 7782 At special positions: 0 Unit cell: (121.426, 121.426, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 8 15.00 Na 2 11.00 O 1224 8.00 N 1188 7.00 C 5336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 274.9 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: 0.15 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: 0.83 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1052 1.30 - 1.43: 2291 1.43 - 1.55: 4540 1.55 - 1.68: 57 1.68 - 1.81: 48 Bond restraints: 7988 Sorted by residual: bond pdb=" C31 POV F 302 " pdb=" O31 POV F 302 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C31 POV A 301 " pdb=" O31 POV A 301 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C31 POV D 301 " pdb=" O31 POV D 301 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C31 POV E 302 " pdb=" O31 POV E 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C21 POV E 302 " pdb=" O21 POV E 302 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 7983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 10259 2.39 - 4.79: 367 4.79 - 7.18: 114 7.18 - 9.58: 44 9.58 - 11.97: 20 Bond angle restraints: 10804 Sorted by residual: angle pdb=" C ASN E 79 " pdb=" N PRO E 80 " pdb=" CA PRO E 80 " ideal model delta sigma weight residual 119.84 131.81 -11.97 1.25e+00 6.40e-01 9.18e+01 angle pdb=" C ASN F 79 " pdb=" N PRO F 80 " pdb=" CA PRO F 80 " ideal model delta sigma weight residual 119.84 131.81 -11.97 1.25e+00 6.40e-01 9.17e+01 angle pdb=" C ASN A 79 " pdb=" N PRO A 80 " pdb=" CA PRO A 80 " ideal model delta sigma weight residual 119.84 131.78 -11.94 1.25e+00 6.40e-01 9.13e+01 angle pdb=" C ASN D 79 " pdb=" N PRO D 80 " pdb=" CA PRO D 80 " ideal model delta sigma weight residual 119.84 131.78 -11.94 1.25e+00 6.40e-01 9.12e+01 angle pdb=" N VAL E 197 " pdb=" CA VAL E 197 " pdb=" C VAL E 197 " ideal model delta sigma weight residual 110.72 118.38 -7.66 1.01e+00 9.80e-01 5.75e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 3948 23.68 - 47.37: 544 47.37 - 71.05: 136 71.05 - 94.73: 36 94.73 - 118.41: 4 Dihedral angle restraints: 4668 sinusoidal: 2020 harmonic: 2648 Sorted by residual: dihedral pdb=" C29 POV E 302 " pdb="C210 POV E 302 " pdb="C211 POV E 302 " pdb="C212 POV E 302 " ideal model delta sinusoidal sigma weight residual 112.25 -129.34 -118.41 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C29 POV A 301 " pdb="C210 POV A 301 " pdb="C211 POV A 301 " pdb="C212 POV A 301 " ideal model delta sinusoidal sigma weight residual 112.25 -129.35 -118.40 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C29 POV D 301 " pdb="C210 POV D 301 " pdb="C211 POV D 301 " pdb="C212 POV D 301 " ideal model delta sinusoidal sigma weight residual 112.25 -129.36 -118.39 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 935 0.052 - 0.104: 261 0.104 - 0.156: 32 0.156 - 0.209: 0 0.209 - 0.261: 4 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CA MET E 198 " pdb=" N MET E 198 " pdb=" C MET E 198 " pdb=" CB MET E 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET F 198 " pdb=" N MET F 198 " pdb=" C MET F 198 " pdb=" CB MET F 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET A 198 " pdb=" N MET A 198 " pdb=" C MET A 198 " pdb=" CB MET A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1229 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 199 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO F 200 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 199 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 200 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 199 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.52e+00 pdb=" N PRO E 200 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 200 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 200 " 0.037 5.00e-02 4.00e+02 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1122 2.74 - 3.28: 7813 3.28 - 3.82: 12303 3.82 - 4.36: 14717 4.36 - 4.90: 24876 Nonbonded interactions: 60831 Sorted by model distance: nonbonded pdb=" O SER D 78 " pdb=" OG SER D 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER F 78 " pdb=" OG SER F 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER E 78 " pdb=" OG SER E 78 " model vdw 2.201 3.040 nonbonded pdb=" O PHE A 158 " pdb=" OH TYR A 211 " model vdw 2.277 3.040 ... (remaining 60826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 13 through 302) selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.098 7988 Z= 0.507 Angle : 1.291 11.973 10804 Z= 0.639 Chirality : 0.047 0.261 1232 Planarity : 0.006 0.064 1256 Dihedral : 22.960 118.414 2940 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.07 % Favored : 91.48 % Rotamer: Outliers : 15.83 % Allowed : 15.83 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.22), residues: 892 helix: -2.52 (0.15), residues: 644 sheet: None (None), residues: 0 loop : -3.55 (0.32), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.007 0.001 TYR D 156 PHE 0.012 0.001 PHE D 174 TRP 0.006 0.001 TRP A 91 HIS 0.001 0.000 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.01056 ( 7988) covalent geometry : angle 1.29073 (10804) hydrogen bonds : bond 0.20341 ( 428) hydrogen bonds : angle 8.81949 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 175 time to evaluate : 0.249 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: 0.8390 (tm-30) cc_final: 0.7911 (tm-30) outliers start: 126 outliers final: 83 residues processed: 263 average time/residue: 0.0716 time to fit residues: 26.5666 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 : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 235 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 167 GLN A 186 GLN A 234 ASN D 90 ASN D 167 GLN D 186 GLN D 234 ASN E 90 ASN E 167 GLN E 186 GLN E 234 ASN F 90 ASN F 167 GLN F 186 GLN F 234 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.136404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101926 restraints weight = 11878.409| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.98 r_work: 0.3165 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7988 Z= 0.150 Angle : 0.613 10.615 10804 Z= 0.316 Chirality : 0.040 0.195 1232 Planarity : 0.006 0.056 1256 Dihedral : 21.603 108.361 1477 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.17 % Favored : 92.38 % Rotamer: Outliers : 8.67 % Allowed : 18.59 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.27), residues: 892 helix: -0.34 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.006 0.001 TYR D 156 PHE 0.015 0.001 PHE F 215 TRP 0.022 0.001 TRP D 54 HIS 0.001 0.000 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7988) covalent geometry : angle 0.61308 (10804) hydrogen bonds : bond 0.04529 ( 428) hydrogen bonds : angle 4.80101 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 167 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7240 (ppp) cc_final: 0.6144 (ppp) REVERT: A 22 HIS cc_start: 0.7755 (t-90) cc_final: 0.7372 (t70) REVERT: A 74 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8121 (ttp-110) REVERT: A 191 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 210 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8578 (tp) REVERT: D 16 MET cc_start: 0.7449 (ppp) cc_final: 0.6431 (ppp) REVERT: D 22 HIS cc_start: 0.7767 (t-90) cc_final: 0.7367 (t70) REVERT: D 74 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8118 (ttp-110) REVERT: D 191 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7809 (tm-30) REVERT: E 16 MET cc_start: 0.7337 (ppp) cc_final: 0.7125 (ppp) REVERT: E 22 HIS cc_start: 0.7708 (t-90) cc_final: 0.7281 (t70) REVERT: E 191 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7830 (tm-30) REVERT: F 16 MET cc_start: 0.7403 (ppp) cc_final: 0.6505 (ppp) REVERT: F 22 HIS cc_start: 0.7720 (t-90) cc_final: 0.7288 (t70) REVERT: F 74 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8090 (ttp-110) REVERT: F 191 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7783 (tm-30) REVERT: F 210 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8544 (tp) outliers start: 69 outliers final: 33 residues processed: 222 average time/residue: 0.0869 time to fit residues: 26.0340 Evaluate side-chains 202 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.137864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103941 restraints weight = 11818.447| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.87 r_work: 0.3212 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7988 Z= 0.119 Angle : 0.532 6.523 10804 Z= 0.274 Chirality : 0.039 0.193 1232 Planarity : 0.005 0.051 1256 Dihedral : 19.565 97.825 1362 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.72 % Favored : 93.83 % Rotamer: Outliers : 8.29 % Allowed : 18.72 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.29), residues: 892 helix: 0.54 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.66 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 122 TYR 0.006 0.001 TYR D 49 PHE 0.016 0.001 PHE E 215 TRP 0.002 0.000 TRP D 193 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7988) covalent geometry : angle 0.53231 (10804) hydrogen bonds : bond 0.03738 ( 428) hydrogen bonds : angle 4.20105 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 187 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7659 (t-90) cc_final: 0.7267 (t-170) REVERT: A 42 ILE cc_start: 0.9485 (tt) cc_final: 0.9254 (tt) REVERT: A 73 MET cc_start: 0.8738 (mtp) cc_final: 0.8537 (mtp) REVERT: A 74 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8148 (ttp-110) REVERT: A 90 ASN cc_start: 0.9032 (m-40) cc_final: 0.8711 (m110) REVERT: A 131 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8508 (ttm170) REVERT: A 191 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8100 (tm-30) REVERT: D 16 MET cc_start: 0.6634 (ppp) cc_final: 0.6196 (ppp) REVERT: D 22 HIS cc_start: 0.7644 (t-90) cc_final: 0.7233 (t-170) REVERT: D 42 ILE cc_start: 0.9473 (tt) cc_final: 0.9246 (tt) REVERT: D 73 MET cc_start: 0.8872 (mtp) cc_final: 0.8666 (mtp) REVERT: D 131 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8460 (ttm170) REVERT: D 191 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8115 (tm-30) REVERT: E 22 HIS cc_start: 0.7663 (t-90) cc_final: 0.7165 (t70) REVERT: E 42 ILE cc_start: 0.9476 (tt) cc_final: 0.9257 (tt) REVERT: E 191 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7742 (tm-30) REVERT: F 22 HIS cc_start: 0.7697 (t-90) cc_final: 0.7279 (t-170) REVERT: F 42 ILE cc_start: 0.9470 (tt) cc_final: 0.9267 (tt) REVERT: F 74 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8156 (ttp-110) REVERT: F 90 ASN cc_start: 0.9048 (m-40) cc_final: 0.8726 (m110) REVERT: F 191 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8149 (tm-30) outliers start: 66 outliers final: 46 residues processed: 230 average time/residue: 0.0733 time to fit residues: 23.6165 Evaluate side-chains 222 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 4 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.138878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104962 restraints weight = 12010.934| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.94 r_work: 0.3216 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7988 Z= 0.114 Angle : 0.594 12.876 10804 Z= 0.280 Chirality : 0.040 0.220 1232 Planarity : 0.008 0.116 1256 Dihedral : 18.682 91.894 1354 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.83 % Favored : 93.72 % Rotamer: Outliers : 7.16 % Allowed : 19.85 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.29), residues: 892 helix: 0.98 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.59 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.006 0.001 TYR E 211 PHE 0.021 0.001 PHE D 215 TRP 0.003 0.000 TRP D 54 HIS 0.000 0.000 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 7988) covalent geometry : angle 0.59426 (10804) hydrogen bonds : bond 0.03511 ( 428) hydrogen bonds : angle 4.01351 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6926 (ppp) cc_final: 0.6152 (ppp) REVERT: A 22 HIS cc_start: 0.7604 (t-90) cc_final: 0.7216 (t-170) REVERT: A 42 ILE cc_start: 0.9498 (tt) cc_final: 0.9227 (tt) REVERT: A 90 ASN cc_start: 0.9081 (m-40) cc_final: 0.8746 (m110) REVERT: A 191 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 210 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8482 (tp) REVERT: D 22 HIS cc_start: 0.7641 (t-90) cc_final: 0.7244 (t-170) REVERT: D 42 ILE cc_start: 0.9493 (tt) cc_final: 0.9224 (tt) REVERT: D 73 MET cc_start: 0.8876 (mtp) cc_final: 0.8667 (mtp) REVERT: D 74 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8185 (ttp-110) REVERT: D 102 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8426 (pt) REVERT: D 191 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 22 HIS cc_start: 0.7704 (t-90) cc_final: 0.7258 (t-170) REVERT: E 42 ILE cc_start: 0.9496 (tt) cc_final: 0.9229 (tt) REVERT: E 73 MET cc_start: 0.8879 (mtp) cc_final: 0.8651 (mtp) REVERT: E 191 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8075 (tm-30) REVERT: F 16 MET cc_start: 0.6904 (ppp) cc_final: 0.6042 (ppp) REVERT: F 22 HIS cc_start: 0.7618 (t-90) cc_final: 0.7213 (t-170) REVERT: F 42 ILE cc_start: 0.9488 (tt) cc_final: 0.9282 (tt) REVERT: F 74 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8097 (ttp-110) REVERT: F 90 ASN cc_start: 0.9070 (m-40) cc_final: 0.8714 (m110) REVERT: F 191 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8103 (tm-30) REVERT: F 210 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8495 (tp) outliers start: 57 outliers final: 37 residues processed: 216 average time/residue: 0.0713 time to fit residues: 22.0464 Evaluate side-chains 212 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 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 102 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 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 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 210 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.138042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103497 restraints weight = 11952.356| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.95 r_work: 0.3176 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7988 Z= 0.154 Angle : 0.593 15.120 10804 Z= 0.294 Chirality : 0.041 0.253 1232 Planarity : 0.004 0.038 1256 Dihedral : 18.413 92.607 1344 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 7.41 % Allowed : 20.10 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.29 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.29), residues: 892 helix: 1.12 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.69 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 74 TYR 0.008 0.001 TYR D 211 PHE 0.022 0.001 PHE E 215 TRP 0.003 0.001 TRP E 91 HIS 0.001 0.000 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7988) covalent geometry : angle 0.59311 (10804) hydrogen bonds : bond 0.03690 ( 428) hydrogen bonds : angle 4.17336 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6982 (ppp) cc_final: 0.6374 (ppp) REVERT: A 22 HIS cc_start: 0.7558 (t-90) cc_final: 0.7189 (t-170) REVERT: A 42 ILE cc_start: 0.9493 (tt) cc_final: 0.9285 (tt) REVERT: A 90 ASN cc_start: 0.9117 (m-40) cc_final: 0.8876 (m-40) REVERT: A 191 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 210 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8621 (tp) REVERT: D 22 HIS cc_start: 0.7718 (t-90) cc_final: 0.7295 (t-170) REVERT: D 38 LEU cc_start: 0.9414 (tt) cc_final: 0.9213 (tp) REVERT: D 42 ILE cc_start: 0.9485 (tt) cc_final: 0.9275 (tt) REVERT: D 73 MET cc_start: 0.8897 (mtp) cc_final: 0.8668 (mtp) REVERT: D 74 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8229 (ttp-110) REVERT: D 191 GLU cc_start: 0.8669 (tm-30) cc_final: 0.7876 (tm-30) REVERT: E 22 HIS cc_start: 0.7677 (t-90) cc_final: 0.7220 (t-170) REVERT: E 42 ILE cc_start: 0.9486 (tt) cc_final: 0.9280 (tt) REVERT: E 73 MET cc_start: 0.8841 (mtp) cc_final: 0.8623 (mtp) REVERT: E 191 GLU cc_start: 0.8681 (tm-30) cc_final: 0.7933 (tm-30) REVERT: F 16 MET cc_start: 0.7031 (ppp) cc_final: 0.6401 (ppp) REVERT: F 22 HIS cc_start: 0.7611 (t-90) cc_final: 0.7211 (t-170) REVERT: F 74 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8176 (ttp-110) REVERT: F 90 ASN cc_start: 0.9083 (m-40) cc_final: 0.8827 (m-40) REVERT: F 191 GLU cc_start: 0.8625 (tm-30) cc_final: 0.7784 (tm-30) REVERT: F 210 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8637 (tp) outliers start: 59 outliers final: 45 residues processed: 221 average time/residue: 0.0627 time to fit residues: 20.5312 Evaluate side-chains 223 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 235 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.137498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103040 restraints weight = 11846.975| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.93 r_work: 0.3188 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7988 Z= 0.155 Angle : 0.589 10.600 10804 Z= 0.292 Chirality : 0.042 0.236 1232 Planarity : 0.004 0.037 1256 Dihedral : 18.200 94.303 1344 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.66 % Allowed : 20.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.29), residues: 892 helix: 1.22 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.84 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 74 TYR 0.008 0.001 TYR D 211 PHE 0.021 0.001 PHE F 215 TRP 0.003 0.001 TRP E 193 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7988) covalent geometry : angle 0.58878 (10804) hydrogen bonds : bond 0.03701 ( 428) hydrogen bonds : angle 4.18038 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.6842 (ppp) cc_final: 0.6370 (ppp) REVERT: A 22 HIS cc_start: 0.7539 (t-90) cc_final: 0.7179 (t-170) REVERT: A 90 ASN cc_start: 0.9108 (m-40) cc_final: 0.8869 (m-40) REVERT: A 191 GLU cc_start: 0.8651 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 210 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8668 (tp) REVERT: D 16 MET cc_start: 0.7319 (ppp) cc_final: 0.7036 (ppp) REVERT: D 22 HIS cc_start: 0.7583 (t-90) cc_final: 0.7226 (t-170) REVERT: D 73 MET cc_start: 0.8873 (mtp) cc_final: 0.8639 (mtp) REVERT: D 74 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8212 (ttp-110) REVERT: D 90 ASN cc_start: 0.9182 (m-40) cc_final: 0.8957 (m-40) REVERT: D 191 GLU cc_start: 0.8680 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 22 HIS cc_start: 0.7492 (t-90) cc_final: 0.7076 (t-170) REVERT: E 73 MET cc_start: 0.8817 (mtp) cc_final: 0.8587 (mtp) REVERT: E 191 GLU cc_start: 0.8665 (tm-30) cc_final: 0.7942 (tm-30) REVERT: F 16 MET cc_start: 0.6796 (ppp) cc_final: 0.6363 (ppp) REVERT: F 22 HIS cc_start: 0.7581 (t-90) cc_final: 0.7194 (t-170) REVERT: F 74 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8135 (ttp-110) REVERT: F 90 ASN cc_start: 0.9121 (m-40) cc_final: 0.8904 (m-40) REVERT: F 191 GLU cc_start: 0.8624 (tm-30) cc_final: 0.7822 (tm-30) REVERT: F 210 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8674 (tp) outliers start: 61 outliers final: 49 residues processed: 215 average time/residue: 0.0619 time to fit residues: 19.7094 Evaluate side-chains 224 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 95 LEU Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 40 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 81 optimal weight: 0.0000 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104953 restraints weight = 11843.772| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.87 r_work: 0.3269 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7988 Z= 0.119 Angle : 0.591 13.520 10804 Z= 0.284 Chirality : 0.041 0.209 1232 Planarity : 0.004 0.036 1256 Dihedral : 17.759 89.331 1344 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.66 % Allowed : 20.60 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.29), residues: 892 helix: 1.42 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.89 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 58 TYR 0.007 0.001 TYR D 211 PHE 0.019 0.001 PHE E 215 TRP 0.003 0.000 TRP E 193 HIS 0.001 0.000 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7988) covalent geometry : angle 0.59148 (10804) hydrogen bonds : bond 0.03425 ( 428) hydrogen bonds : angle 4.07547 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.287 Fit side-chains REVERT: A 16 MET cc_start: 0.6751 (ppp) cc_final: 0.6414 (ppp) REVERT: A 22 HIS cc_start: 0.7475 (t-90) cc_final: 0.7183 (t-170) REVERT: A 90 ASN cc_start: 0.9126 (m-40) cc_final: 0.8905 (m-40) REVERT: A 191 GLU cc_start: 0.8558 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 210 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8559 (tp) REVERT: A 220 THR cc_start: 0.9358 (m) cc_final: 0.9016 (m) REVERT: D 22 HIS cc_start: 0.7518 (t-90) cc_final: 0.7208 (t-170) REVERT: D 73 MET cc_start: 0.8796 (mtp) cc_final: 0.8550 (mtp) REVERT: D 220 THR cc_start: 0.9346 (m) cc_final: 0.8985 (m) REVERT: E 22 HIS cc_start: 0.7512 (t-90) cc_final: 0.7145 (t-170) REVERT: E 73 MET cc_start: 0.8738 (mtp) cc_final: 0.8484 (mtp) REVERT: E 220 THR cc_start: 0.9361 (m) cc_final: 0.9037 (m) REVERT: F 16 MET cc_start: 0.6663 (ppp) cc_final: 0.6384 (ppp) REVERT: F 22 HIS cc_start: 0.7484 (t-90) cc_final: 0.7219 (t-170) REVERT: F 74 ARG cc_start: 0.8548 (ttm-80) cc_final: 0.8102 (ttp-110) REVERT: F 90 ASN cc_start: 0.9124 (m-40) cc_final: 0.8826 (m110) REVERT: F 191 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8131 (tm-30) REVERT: F 210 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8603 (tp) REVERT: F 220 THR cc_start: 0.9363 (m) cc_final: 0.9036 (m) outliers start: 53 outliers final: 43 residues processed: 220 average time/residue: 0.0645 time to fit residues: 20.2682 Evaluate side-chains 229 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 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 210 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3856 r_free = 0.3856 target = 0.138517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104122 restraints weight = 11908.503| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.93 r_work: 0.3190 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7988 Z= 0.161 Angle : 0.649 18.963 10804 Z= 0.310 Chirality : 0.043 0.205 1232 Planarity : 0.004 0.035 1256 Dihedral : 17.803 89.891 1344 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.41 % Allowed : 20.98 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.29), residues: 892 helix: 1.39 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.90 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 116 TYR 0.008 0.001 TYR E 211 PHE 0.020 0.001 PHE F 215 TRP 0.003 0.001 TRP F 209 HIS 0.001 0.000 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7988) covalent geometry : angle 0.64906 (10804) hydrogen bonds : bond 0.03659 ( 428) hydrogen bonds : angle 4.22778 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 0.287 Fit side-chains REVERT: A 16 MET cc_start: 0.6560 (ppp) cc_final: 0.6335 (ppp) REVERT: A 22 HIS cc_start: 0.7276 (t-90) cc_final: 0.7031 (t-170) REVERT: A 191 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 210 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8583 (tp) REVERT: A 220 THR cc_start: 0.9284 (m) cc_final: 0.8943 (m) REVERT: D 22 HIS cc_start: 0.7492 (t-90) cc_final: 0.7220 (t-170) REVERT: D 73 MET cc_start: 0.8733 (mtp) cc_final: 0.8461 (mtp) REVERT: D 74 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8099 (ttp-110) REVERT: D 191 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7765 (tm-30) REVERT: D 220 THR cc_start: 0.9273 (m) cc_final: 0.8892 (m) REVERT: E 22 HIS cc_start: 0.7304 (t-90) cc_final: 0.7002 (t-170) REVERT: E 73 MET cc_start: 0.8689 (mtp) cc_final: 0.8439 (mtp) REVERT: E 74 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.8135 (ttp-110) REVERT: E 191 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7805 (tm-30) REVERT: E 220 THR cc_start: 0.9272 (m) cc_final: 0.8940 (m) REVERT: F 16 MET cc_start: 0.6578 (ppp) cc_final: 0.6376 (ppp) REVERT: F 22 HIS cc_start: 0.7389 (t-90) cc_final: 0.7173 (t-170) REVERT: F 74 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.7999 (ttp-110) REVERT: F 90 ASN cc_start: 0.9071 (m-40) cc_final: 0.8764 (m110) REVERT: F 191 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7719 (tm-30) REVERT: F 210 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8582 (tp) REVERT: F 220 THR cc_start: 0.9285 (m) cc_final: 0.8941 (m) outliers start: 51 outliers final: 45 residues processed: 218 average time/residue: 0.0644 time to fit residues: 20.6035 Evaluate side-chains 234 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 0.8980 chunk 81 optimal weight: 0.0060 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.138922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105209 restraints weight = 11877.466| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.87 r_work: 0.3235 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7988 Z= 0.125 Angle : 0.612 13.452 10804 Z= 0.294 Chirality : 0.041 0.198 1232 Planarity : 0.004 0.036 1256 Dihedral : 17.497 89.443 1344 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.78 % Allowed : 21.23 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.29), residues: 892 helix: 1.48 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.84 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.007 0.001 TYR F 211 PHE 0.019 0.001 PHE E 215 TRP 0.003 0.001 TRP E 193 HIS 0.001 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7988) covalent geometry : angle 0.61167 (10804) hydrogen bonds : bond 0.03423 ( 428) hydrogen bonds : angle 4.12336 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.278 Fit side-chains REVERT: A 22 HIS cc_start: 0.7359 (t-90) cc_final: 0.7048 (t-170) REVERT: A 191 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 210 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 220 THR cc_start: 0.9273 (m) cc_final: 0.8934 (m) REVERT: D 22 HIS cc_start: 0.7493 (t-90) cc_final: 0.7185 (t-170) REVERT: D 73 MET cc_start: 0.8772 (mtp) cc_final: 0.8495 (mtp) REVERT: D 220 THR cc_start: 0.9328 (m) cc_final: 0.8981 (m) REVERT: E 22 HIS cc_start: 0.7495 (t-90) cc_final: 0.7132 (t-170) REVERT: E 73 MET cc_start: 0.8740 (mtp) cc_final: 0.8477 (mtp) REVERT: E 74 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8206 (ttp-110) REVERT: E 220 THR cc_start: 0.9288 (m) cc_final: 0.8965 (m) REVERT: F 16 MET cc_start: 0.6642 (ppp) cc_final: 0.6440 (ppp) REVERT: F 22 HIS cc_start: 0.7549 (t-90) cc_final: 0.7281 (t-170) REVERT: F 74 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8083 (ttp-110) REVERT: F 90 ASN cc_start: 0.9101 (m-40) cc_final: 0.8816 (m110) REVERT: F 210 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8636 (tp) REVERT: F 220 THR cc_start: 0.9308 (m) cc_final: 0.8965 (m) outliers start: 54 outliers final: 47 residues processed: 218 average time/residue: 0.0599 time to fit residues: 19.4374 Evaluate side-chains 232 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 40 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 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.139145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105140 restraints weight = 11927.982| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.92 r_work: 0.3219 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7988 Z= 0.129 Angle : 0.662 19.309 10804 Z= 0.310 Chirality : 0.041 0.195 1232 Planarity : 0.004 0.036 1256 Dihedral : 17.048 88.300 1335 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.66 % Allowed : 22.11 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.29), residues: 892 helix: 1.53 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.74 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.007 0.001 TYR F 211 PHE 0.019 0.001 PHE E 215 TRP 0.004 0.001 TRP A 89 HIS 0.001 0.000 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7988) covalent geometry : angle 0.66180 (10804) hydrogen bonds : bond 0.03446 ( 428) hydrogen bonds : angle 4.11480 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.244 Fit side-chains REVERT: A 22 HIS cc_start: 0.7425 (t-90) cc_final: 0.7112 (t-170) REVERT: A 191 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 210 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 220 THR cc_start: 0.9269 (m) cc_final: 0.8936 (m) REVERT: D 22 HIS cc_start: 0.7463 (t-90) cc_final: 0.7164 (t-170) REVERT: D 191 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 220 THR cc_start: 0.9320 (m) cc_final: 0.8981 (m) REVERT: E 22 HIS cc_start: 0.7488 (t-90) cc_final: 0.7124 (t-170) REVERT: E 73 MET cc_start: 0.8753 (mtp) cc_final: 0.8479 (mtp) REVERT: E 220 THR cc_start: 0.9280 (m) cc_final: 0.8947 (m) REVERT: F 22 HIS cc_start: 0.7539 (t-90) cc_final: 0.7205 (t-170) REVERT: F 90 ASN cc_start: 0.9096 (m-40) cc_final: 0.8820 (m110) REVERT: F 210 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8630 (tp) REVERT: F 220 THR cc_start: 0.9284 (m) cc_final: 0.8949 (m) outliers start: 53 outliers final: 49 residues processed: 213 average time/residue: 0.0597 time to fit residues: 19.0654 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 : 0.296 ------------------------------------------------------------------------------- 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 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 40 VAL Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 40 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 195 SER Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 226 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.139044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.105431 restraints weight = 11792.307| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.90 r_work: 0.3227 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7988 Z= 0.131 Angle : 0.674 19.493 10804 Z= 0.315 Chirality : 0.042 0.195 1232 Planarity : 0.004 0.036 1256 Dihedral : 16.886 87.500 1332 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.53 % Allowed : 22.36 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.30), residues: 892 helix: 1.55 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.59 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 74 TYR 0.007 0.001 TYR E 211 PHE 0.019 0.001 PHE F 215 TRP 0.010 0.001 TRP F 65 HIS 0.001 0.000 HIS F 22 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7988) covalent geometry : angle 0.67438 (10804) hydrogen bonds : bond 0.03461 ( 428) hydrogen bonds : angle 4.11646 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.68 seconds wall clock time: 38 minutes 33.77 seconds (2313.77 seconds total)