Starting phenix.real_space_refine on Wed Mar 12 15:34:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwx_21425/03_2025/6vwx_21425_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwx_21425/03_2025/6vwx_21425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vwx_21425/03_2025/6vwx_21425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwx_21425/03_2025/6vwx_21425.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwx_21425/03_2025/6vwx_21425_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwx_21425/03_2025/6vwx_21425_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 24 5.16 5 Na 2 4.78 5 C 5336 2.51 5 N 1188 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7782 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "E" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' NA': 2, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, F Time building chain proxies: 5.72, per 1000 atoms: 0.74 Number of scatterers: 7782 At special positions: 0 Unit cell: (121.426, 121.426, 65.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 8 15.00 Na 2 11.00 O 1224 8.00 N 1188 7.00 C 5336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 22 through 43 removed outlier: 3.811A pdb=" N THR A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 55 through 77 removed outlier: 3.881A pdb=" N ALA A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.750A pdb=" N TRP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.670A pdb=" N ARG A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.513A pdb=" N ARG A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 164 removed outlier: 3.763A pdb=" N LEU A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.558A pdb=" N VAL A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.724A pdb=" N GLU A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 237 removed outlier: 3.507A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 43 removed outlier: 3.812A pdb=" N THR D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 Processing helix chain 'D' and resid 55 through 77 removed outlier: 3.882A pdb=" N ALA D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 103 removed outlier: 3.750A pdb=" N TRP D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 122 removed outlier: 3.670A pdb=" N ARG D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.512A pdb=" N ARG D 132 " --> pdb=" O PRO D 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 133 " --> pdb=" O SER D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 164 removed outlier: 3.763A pdb=" N LEU D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.558A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.724A pdb=" N GLU D 204 " --> pdb=" O PRO D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 237 removed outlier: 3.506A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 43 removed outlier: 3.812A pdb=" N THR E 26 " --> pdb=" O HIS E 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE E 27 " --> pdb=" O ARG E 23 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 52 Processing helix chain 'E' and resid 55 through 77 removed outlier: 3.881A pdb=" N ALA E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 103 removed outlier: 3.751A pdb=" N TRP E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 122 removed outlier: 3.670A pdb=" N ARG E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 127 through 139 removed outlier: 3.513A pdb=" N ARG E 132 " --> pdb=" O PRO E 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 164 removed outlier: 3.763A pdb=" N LEU E 148 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE E 149 " --> pdb=" O GLY E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 189 removed outlier: 3.558A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.725A pdb=" N GLU E 204 " --> pdb=" O PRO E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 237 removed outlier: 3.507A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 43 removed outlier: 3.811A pdb=" N THR F 26 " --> pdb=" O HIS F 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE F 27 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU F 43 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 52 Processing helix chain 'F' and resid 55 through 77 removed outlier: 3.881A pdb=" N ALA F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 103 removed outlier: 3.750A pdb=" N TRP F 91 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 removed outlier: 3.670A pdb=" N ARG F 113 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU F 115 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 127 through 139 removed outlier: 3.513A pdb=" N ARG F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 164 removed outlier: 3.763A pdb=" N LEU F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE F 149 " --> pdb=" O GLY F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 189 removed outlier: 3.559A pdb=" N VAL F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 189 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.725A pdb=" N GLU F 204 " --> pdb=" O PRO F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 237 removed outlier: 3.506A pdb=" N PHE F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 223 " --> pdb=" O GLY F 219 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1052 1.30 - 1.43: 2291 1.43 - 1.55: 4540 1.55 - 1.68: 57 1.68 - 1.81: 48 Bond restraints: 7988 Sorted by residual: bond pdb=" C31 POV F 302 " pdb=" O31 POV F 302 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C31 POV A 301 " pdb=" O31 POV A 301 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C31 POV D 301 " pdb=" O31 POV D 301 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C31 POV E 302 " pdb=" O31 POV E 302 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C21 POV E 302 " pdb=" O21 POV E 302 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 7983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 10259 2.39 - 4.79: 367 4.79 - 7.18: 114 7.18 - 9.58: 44 9.58 - 11.97: 20 Bond angle restraints: 10804 Sorted by residual: angle pdb=" C ASN E 79 " pdb=" N PRO E 80 " pdb=" CA PRO E 80 " ideal model delta sigma weight residual 119.84 131.81 -11.97 1.25e+00 6.40e-01 9.18e+01 angle pdb=" C ASN F 79 " pdb=" N PRO F 80 " pdb=" CA PRO F 80 " ideal model delta sigma weight residual 119.84 131.81 -11.97 1.25e+00 6.40e-01 9.17e+01 angle pdb=" C ASN A 79 " pdb=" N PRO A 80 " pdb=" CA PRO A 80 " ideal model delta sigma weight residual 119.84 131.78 -11.94 1.25e+00 6.40e-01 9.13e+01 angle pdb=" C ASN D 79 " pdb=" N PRO D 80 " pdb=" CA PRO D 80 " ideal model delta sigma weight residual 119.84 131.78 -11.94 1.25e+00 6.40e-01 9.12e+01 angle pdb=" N VAL E 197 " pdb=" CA VAL E 197 " pdb=" C VAL E 197 " ideal model delta sigma weight residual 110.72 118.38 -7.66 1.01e+00 9.80e-01 5.75e+01 ... (remaining 10799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 3948 23.68 - 47.37: 544 47.37 - 71.05: 136 71.05 - 94.73: 36 94.73 - 118.41: 4 Dihedral angle restraints: 4668 sinusoidal: 2020 harmonic: 2648 Sorted by residual: dihedral pdb=" C29 POV E 302 " pdb="C210 POV E 302 " pdb="C211 POV E 302 " pdb="C212 POV E 302 " ideal model delta sinusoidal sigma weight residual 112.25 -129.34 -118.41 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C29 POV A 301 " pdb="C210 POV A 301 " pdb="C211 POV A 301 " pdb="C212 POV A 301 " ideal model delta sinusoidal sigma weight residual 112.25 -129.35 -118.40 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C29 POV D 301 " pdb="C210 POV D 301 " pdb="C211 POV D 301 " pdb="C212 POV D 301 " ideal model delta sinusoidal sigma weight residual 112.25 -129.36 -118.39 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 4665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 935 0.052 - 0.104: 261 0.104 - 0.156: 32 0.156 - 0.209: 0 0.209 - 0.261: 4 Chirality restraints: 1232 Sorted by residual: chirality pdb=" CA MET E 198 " pdb=" N MET E 198 " pdb=" C MET E 198 " pdb=" CB MET E 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET F 198 " pdb=" N MET F 198 " pdb=" C MET F 198 " pdb=" CB MET F 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET A 198 " pdb=" N MET A 198 " pdb=" C MET A 198 " pdb=" CB MET A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1229 not shown) Planarity restraints: 1256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 199 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO F 200 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 200 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 199 " -0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 200 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 199 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.52e+00 pdb=" N PRO E 200 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 200 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 200 " 0.037 5.00e-02 4.00e+02 ... (remaining 1253 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1122 2.74 - 3.28: 7813 3.28 - 3.82: 12303 3.82 - 4.36: 14717 4.36 - 4.90: 24876 Nonbonded interactions: 60831 Sorted by model distance: nonbonded pdb=" O SER D 78 " pdb=" OG SER D 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER F 78 " pdb=" OG SER F 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.200 3.040 nonbonded pdb=" O SER E 78 " pdb=" OG SER E 78 " model vdw 2.201 3.040 nonbonded pdb=" O PHE A 158 " pdb=" OH TYR A 211 " model vdw 2.277 3.040 ... (remaining 60826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 237 or resid 301 through 302)) selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.350 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.098 7988 Z= 0.675 Angle : 1.291 11.973 10804 Z= 0.639 Chirality : 0.047 0.261 1232 Planarity : 0.006 0.064 1256 Dihedral : 22.960 118.414 2940 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.07 % Favored : 91.48 % Rotamer: Outliers : 15.83 % Allowed : 15.83 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.22), residues: 892 helix: -2.52 (0.15), residues: 644 sheet: None (None), residues: 0 loop : -3.55 (0.32), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 91 HIS 0.001 0.000 HIS F 22 PHE 0.012 0.001 PHE D 174 TYR 0.007 0.001 TYR D 156 ARG 0.002 0.000 ARG F 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 175 time to evaluate : 0.800 Fit side-chains REVERT: A 22 HIS cc_start: 0.7582 (t-90) cc_final: 0.7250 (t-90) REVERT: A 90 ASN cc_start: 0.8947 (m110) cc_final: 0.8691 (m110) REVERT: A 95 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 191 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7978 (tm-30) REVERT: D 22 HIS cc_start: 0.7639 (t-90) cc_final: 0.7290 (t70) REVERT: D 90 ASN cc_start: 0.8931 (m110) cc_final: 0.8659 (m110) REVERT: D 95 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8485 (tp) REVERT: D 191 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7768 (tm-30) REVERT: E 22 HIS cc_start: 0.7651 (t-90) cc_final: 0.7286 (t70) REVERT: E 70 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: E 90 ASN cc_start: 0.8910 (m110) cc_final: 0.8649 (m110) REVERT: E 122 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8431 (ttt-90) REVERT: E 181 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8958 (tt) REVERT: E 191 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7766 (tm-30) REVERT: F 22 HIS cc_start: 0.7615 (t-90) cc_final: 0.7264 (t70) REVERT: F 53 LYS cc_start: 0.8029 (tptp) cc_final: 0.7808 (tptp) REVERT: F 90 ASN cc_start: 0.8934 (m110) cc_final: 0.8685 (m110) REVERT: F 191 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7911 (tm-30) outliers start: 126 outliers final: 83 residues processed: 263 average time/residue: 0.1659 time to fit residues: 60.6194 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 : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 21 ASN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 122 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 198 MET Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 235 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 167 GLN A 186 GLN A 234 ASN D 90 ASN D 167 GLN D 186 GLN D 234 ASN E 90 ASN E 167 GLN E 186 GLN E 234 ASN F 90 ASN F 167 GLN F 186 GLN F 234 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102891 restraints weight = 11694.960| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.96 r_work: 0.3175 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7988 Z= 0.210 Angle : 0.607 10.577 10804 Z= 0.313 Chirality : 0.040 0.191 1232 Planarity : 0.006 0.055 1256 Dihedral : 21.478 107.539 1477 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.17 % Favored : 92.38 % Rotamer: Outliers : 8.42 % Allowed : 18.47 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.27), residues: 892 helix: -0.26 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 54 HIS 0.001 0.000 HIS F 22 PHE 0.015 0.001 PHE F 215 TYR 0.006 0.001 TYR D 156 ARG 0.003 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7244 (ppp) cc_final: 0.6253 (ppp) REVERT: A 22 HIS cc_start: 0.7739 (t-90) cc_final: 0.7377 (t70) REVERT: A 74 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8104 (ttp-110) REVERT: A 90 ASN cc_start: 0.8982 (m-40) cc_final: 0.8697 (m110) REVERT: A 191 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7732 (tm-30) REVERT: D 16 MET cc_start: 0.7450 (ppp) cc_final: 0.6436 (ppp) REVERT: D 22 HIS cc_start: 0.7749 (t-90) cc_final: 0.7360 (t70) REVERT: D 74 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8115 (ttp-110) REVERT: D 191 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7731 (tm-30) REVERT: E 16 MET cc_start: 0.7236 (ppp) cc_final: 0.6942 (ppp) REVERT: E 22 HIS cc_start: 0.7716 (t-90) cc_final: 0.7302 (t70) REVERT: E 70 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: E 93 ASP cc_start: 0.8714 (m-30) cc_final: 0.8476 (m-30) REVERT: E 191 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7775 (tm-30) REVERT: F 16 MET cc_start: 0.7243 (ppp) cc_final: 0.6376 (ppp) REVERT: F 22 HIS cc_start: 0.7700 (t-90) cc_final: 0.7292 (t70) REVERT: F 74 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8113 (ttp-110) REVERT: F 90 ASN cc_start: 0.8968 (m-40) cc_final: 0.8687 (m110) REVERT: F 191 GLU cc_start: 0.8522 (tm-30) cc_final: 0.7738 (tm-30) outliers start: 67 outliers final: 28 residues processed: 225 average time/residue: 0.2152 time to fit residues: 64.8175 Evaluate side-chains 194 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 178 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.0010 chunk 87 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.139476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104829 restraints weight = 11952.491| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.97 r_work: 0.3211 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2501 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= 0.179 Angle : 0.531 6.430 10804 Z= 0.274 Chirality : 0.039 0.194 1232 Planarity : 0.005 0.051 1256 Dihedral : 19.395 96.776 1355 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.83 % Favored : 93.72 % Rotamer: Outliers : 8.17 % Allowed : 18.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 892 helix: 0.58 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.64 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 54 HIS 0.001 0.000 HIS A 101 PHE 0.015 0.001 PHE E 215 TYR 0.006 0.001 TYR E 211 ARG 0.005 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 186 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.6557 (ppp) cc_final: 0.6238 (ppp) REVERT: A 22 HIS cc_start: 0.7479 (t-90) cc_final: 0.7162 (t-170) REVERT: A 42 ILE cc_start: 0.9426 (tt) cc_final: 0.9222 (tt) REVERT: A 73 MET cc_start: 0.8685 (mtp) cc_final: 0.8479 (mtp) REVERT: A 74 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8018 (ttp-110) REVERT: A 90 ASN cc_start: 0.8996 (m-40) cc_final: 0.8671 (m110) REVERT: A 131 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8452 (ttm170) REVERT: A 191 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 210 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8402 (tp) REVERT: D 16 MET cc_start: 0.6611 (ppp) cc_final: 0.6199 (ppp) REVERT: D 22 HIS cc_start: 0.7477 (t-90) cc_final: 0.7151 (t-170) REVERT: D 42 ILE cc_start: 0.9434 (tt) cc_final: 0.9224 (tt) REVERT: D 74 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.8051 (ttp-110) REVERT: D 131 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8442 (ttm170) REVERT: D 191 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7994 (tm-30) REVERT: E 22 HIS cc_start: 0.7495 (t-90) cc_final: 0.7135 (t-170) REVERT: E 73 MET cc_start: 0.8698 (mtp) cc_final: 0.8480 (mtp) REVERT: E 102 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8158 (pt) REVERT: E 191 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7615 (tm-30) REVERT: F 16 MET cc_start: 0.6629 (ppp) cc_final: 0.6259 (ppp) REVERT: F 22 HIS cc_start: 0.7524 (t-90) cc_final: 0.7175 (t-170) REVERT: F 42 ILE cc_start: 0.9438 (tt) cc_final: 0.9238 (tt) REVERT: F 74 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.7970 (ttp-110) REVERT: F 90 ASN cc_start: 0.9007 (m-40) cc_final: 0.8673 (m110) REVERT: F 102 ILE cc_start: 0.8586 (mt) cc_final: 0.8206 (pt) REVERT: F 191 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7993 (tm-30) REVERT: F 210 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8439 (tp) outliers start: 65 outliers final: 46 residues processed: 228 average time/residue: 0.2186 time to fit residues: 67.7436 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 : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 0.0670 chunk 75 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4916 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.139341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105848 restraints weight = 11889.463| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.87 r_work: 0.3233 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7988 Z= 0.153 Angle : 0.561 11.539 10804 Z= 0.270 Chirality : 0.039 0.223 1232 Planarity : 0.007 0.115 1256 Dihedral : 18.498 91.152 1348 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.05 % Favored : 93.50 % Rotamer: Outliers : 6.78 % Allowed : 20.10 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.29), residues: 892 helix: 1.01 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -2.50 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 54 HIS 0.001 0.000 HIS E 22 PHE 0.021 0.001 PHE A 215 TYR 0.006 0.001 TYR D 211 ARG 0.002 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7597 (t-90) cc_final: 0.7213 (t-170) REVERT: A 42 ILE cc_start: 0.9488 (tt) cc_final: 0.9288 (tt) REVERT: A 74 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8423 (ttm-80) REVERT: A 90 ASN cc_start: 0.9096 (m-40) cc_final: 0.8749 (m110) REVERT: A 191 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 22 HIS cc_start: 0.7598 (t-90) cc_final: 0.7223 (t-170) REVERT: D 74 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8423 (ttm-80) REVERT: D 191 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8063 (tm-30) REVERT: E 22 HIS cc_start: 0.7664 (t-90) cc_final: 0.7224 (t-170) REVERT: E 102 ILE cc_start: 0.8614 (mt) cc_final: 0.8323 (pt) REVERT: E 191 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8043 (tm-30) REVERT: F 22 HIS cc_start: 0.7644 (t-90) cc_final: 0.7222 (t-170) REVERT: F 73 MET cc_start: 0.8889 (mtp) cc_final: 0.8607 (mtp) REVERT: F 74 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8419 (ttm-80) REVERT: F 90 ASN cc_start: 0.9050 (m-40) cc_final: 0.8727 (m110) REVERT: F 102 ILE cc_start: 0.8551 (mt) cc_final: 0.8301 (pt) REVERT: F 191 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8048 (tm-30) outliers start: 54 outliers final: 36 residues processed: 220 average time/residue: 0.1827 time to fit residues: 56.4171 Evaluate side-chains 216 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.139244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105464 restraints weight = 11758.949| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.87 r_work: 0.3227 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7988 Z= 0.175 Angle : 0.619 14.483 10804 Z= 0.295 Chirality : 0.041 0.255 1232 Planarity : 0.004 0.037 1256 Dihedral : 18.055 87.857 1344 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 6.41 % Allowed : 19.85 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 14.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.29), residues: 892 helix: 1.24 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.66 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 54 HIS 0.001 0.000 HIS F 22 PHE 0.021 0.001 PHE E 215 TYR 0.007 0.001 TYR A 211 ARG 0.004 0.000 ARG E 116 *********************** 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 233 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7572 (t-90) cc_final: 0.7252 (t-170) REVERT: A 90 ASN cc_start: 0.9129 (m-40) cc_final: 0.8887 (m-40) REVERT: A 191 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8133 (tm-30) REVERT: A 210 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8445 (tp) REVERT: D 22 HIS cc_start: 0.7703 (t-90) cc_final: 0.7314 (t-170) REVERT: D 74 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8371 (ttm-80) REVERT: D 90 ASN cc_start: 0.9176 (m-40) cc_final: 0.8950 (m-40) REVERT: D 191 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8128 (tm-30) REVERT: E 16 MET cc_start: 0.6819 (ppp) cc_final: 0.6019 (ppp) REVERT: E 22 HIS cc_start: 0.7609 (t-90) cc_final: 0.7190 (t-170) REVERT: E 74 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8280 (ttp-110) REVERT: E 90 ASN cc_start: 0.9156 (m-40) cc_final: 0.8906 (m-40) REVERT: E 102 ILE cc_start: 0.8547 (mt) cc_final: 0.8343 (pt) REVERT: E 191 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8091 (tm-30) REVERT: F 22 HIS cc_start: 0.7617 (t-90) cc_final: 0.7262 (t-170) REVERT: F 73 MET cc_start: 0.8902 (mtp) cc_final: 0.8601 (mtp) REVERT: F 191 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8107 (tm-30) REVERT: F 210 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8420 (tp) outliers start: 51 outliers final: 42 residues processed: 213 average time/residue: 0.1571 time to fit residues: 47.2142 Evaluate side-chains 218 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 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 E residue 54 TRP Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.138047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104241 restraints weight = 11836.872| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.87 r_work: 0.3215 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7988 Z= 0.199 Angle : 0.597 14.048 10804 Z= 0.287 Chirality : 0.041 0.246 1232 Planarity : 0.004 0.036 1256 Dihedral : 17.866 88.639 1344 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.54 % Allowed : 19.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.29), residues: 892 helix: 1.28 (0.20), residues: 676 sheet: None (None), residues: 0 loop : -2.85 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 209 HIS 0.000 0.000 HIS A 101 PHE 0.020 0.001 PHE D 215 TYR 0.008 0.001 TYR E 211 ARG 0.004 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.881 Fit side-chains REVERT: A 16 MET cc_start: 0.7264 (ppp) cc_final: 0.6922 (ppp) REVERT: A 22 HIS cc_start: 0.7545 (t-90) cc_final: 0.7220 (t-170) REVERT: A 90 ASN cc_start: 0.9169 (m-40) cc_final: 0.8935 (m-40) REVERT: A 191 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 210 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8493 (tp) REVERT: A 220 THR cc_start: 0.9365 (m) cc_final: 0.9011 (m) REVERT: D 16 MET cc_start: 0.7306 (ppp) cc_final: 0.6988 (ppp) REVERT: D 22 HIS cc_start: 0.7630 (t-90) cc_final: 0.7262 (t-170) REVERT: D 73 MET cc_start: 0.8541 (mtp) cc_final: 0.8336 (mtp) REVERT: D 90 ASN cc_start: 0.9202 (m-40) cc_final: 0.8965 (m-40) REVERT: D 191 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8199 (tm-30) REVERT: D 220 THR cc_start: 0.9337 (m) cc_final: 0.8958 (m) REVERT: E 16 MET cc_start: 0.6460 (ppp) cc_final: 0.6058 (ppp) REVERT: E 22 HIS cc_start: 0.7585 (t-90) cc_final: 0.7163 (t-170) REVERT: E 73 MET cc_start: 0.8869 (mtp) cc_final: 0.8567 (mtp) REVERT: E 74 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8243 (ttp-110) REVERT: E 90 ASN cc_start: 0.9162 (m-40) cc_final: 0.8935 (m-40) REVERT: E 191 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7847 (tm-30) REVERT: E 220 THR cc_start: 0.9363 (m) cc_final: 0.9027 (m) REVERT: F 16 MET cc_start: 0.7391 (ppp) cc_final: 0.7072 (ppp) REVERT: F 22 HIS cc_start: 0.7574 (t-90) cc_final: 0.7221 (t-170) REVERT: F 73 MET cc_start: 0.8858 (mtp) cc_final: 0.8531 (mtp) REVERT: F 90 ASN cc_start: 0.9136 (m-40) cc_final: 0.8902 (m-40) REVERT: F 191 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8088 (tm-30) REVERT: F 210 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8476 (tp) REVERT: F 220 THR cc_start: 0.9358 (m) cc_final: 0.9004 (m) outliers start: 60 outliers final: 48 residues processed: 219 average time/residue: 0.1487 time to fit residues: 47.0443 Evaluate side-chains 227 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 34 LEU Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 75 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.139183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.105570 restraints weight = 11798.733| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.87 r_work: 0.3242 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3151 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= 0.171 Angle : 0.580 9.348 10804 Z= 0.281 Chirality : 0.042 0.257 1232 Planarity : 0.004 0.035 1256 Dihedral : 17.580 89.472 1344 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.66 % Allowed : 19.85 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.29), residues: 892 helix: 1.45 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.91 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 65 HIS 0.001 0.000 HIS D 101 PHE 0.019 0.001 PHE E 215 TYR 0.007 0.001 TYR A 211 ARG 0.004 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.902 Fit side-chains REVERT: A 16 MET cc_start: 0.7286 (ppp) cc_final: 0.6962 (ppp) REVERT: A 22 HIS cc_start: 0.7565 (t-90) cc_final: 0.7250 (t-170) REVERT: A 90 ASN cc_start: 0.9172 (m-40) cc_final: 0.8930 (m110) REVERT: A 191 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 210 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 220 THR cc_start: 0.9345 (m) cc_final: 0.9009 (m) REVERT: D 16 MET cc_start: 0.7286 (ppp) cc_final: 0.7003 (ppp) REVERT: D 22 HIS cc_start: 0.7520 (t-90) cc_final: 0.7198 (t-170) REVERT: D 90 ASN cc_start: 0.9183 (m-40) cc_final: 0.8930 (m110) REVERT: D 191 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 220 THR cc_start: 0.9336 (m) cc_final: 0.8977 (m) REVERT: E 22 HIS cc_start: 0.7516 (t-90) cc_final: 0.7144 (t-170) REVERT: E 73 MET cc_start: 0.8842 (mtp) cc_final: 0.8524 (mtp) REVERT: E 90 ASN cc_start: 0.9145 (m-40) cc_final: 0.8928 (m-40) REVERT: E 191 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7776 (tm-30) REVERT: E 220 THR cc_start: 0.9324 (m) cc_final: 0.8993 (m) REVERT: F 16 MET cc_start: 0.7185 (ppp) cc_final: 0.6769 (ppp) REVERT: F 22 HIS cc_start: 0.7538 (t-90) cc_final: 0.7210 (t-170) REVERT: F 73 MET cc_start: 0.8805 (mtp) cc_final: 0.8455 (mtp) REVERT: F 90 ASN cc_start: 0.9138 (m-40) cc_final: 0.8898 (m110) REVERT: F 191 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8153 (tm-30) REVERT: F 210 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8436 (tp) REVERT: F 220 THR cc_start: 0.9345 (m) cc_final: 0.9003 (m) outliers start: 53 outliers final: 49 residues processed: 214 average time/residue: 0.1571 time to fit residues: 48.9023 Evaluate side-chains 229 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 195 SER 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 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 53 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103652 restraints weight = 11852.253| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.86 r_work: 0.3249 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7988 Z= 0.239 Angle : 0.634 19.259 10804 Z= 0.303 Chirality : 0.042 0.228 1232 Planarity : 0.004 0.035 1256 Dihedral : 17.667 89.496 1344 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 7.04 % Allowed : 19.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.29), residues: 892 helix: 1.43 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.93 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 209 HIS 0.000 0.000 HIS F 101 PHE 0.020 0.001 PHE D 215 TYR 0.009 0.001 TYR E 211 ARG 0.004 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7344 (ppp) cc_final: 0.7081 (ppp) REVERT: A 22 HIS cc_start: 0.7456 (t-90) cc_final: 0.7185 (t-170) REVERT: A 191 GLU cc_start: 0.8619 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 210 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8551 (tp) REVERT: A 220 THR cc_start: 0.9365 (m) cc_final: 0.9021 (m) REVERT: D 16 MET cc_start: 0.7196 (ppp) cc_final: 0.6952 (ppp) REVERT: D 22 HIS cc_start: 0.7491 (t-90) cc_final: 0.7192 (t-170) REVERT: D 191 GLU cc_start: 0.8693 (tm-30) cc_final: 0.7992 (tm-30) REVERT: D 220 THR cc_start: 0.9363 (m) cc_final: 0.9003 (m) REVERT: E 22 HIS cc_start: 0.7523 (t-90) cc_final: 0.7179 (t-170) REVERT: E 73 MET cc_start: 0.8831 (mtp) cc_final: 0.8491 (mtp) REVERT: E 191 GLU cc_start: 0.8646 (tm-30) cc_final: 0.7962 (tm-30) REVERT: E 220 THR cc_start: 0.9345 (m) cc_final: 0.9024 (m) REVERT: F 16 MET cc_start: 0.7133 (ppp) cc_final: 0.6813 (ppp) REVERT: F 22 HIS cc_start: 0.7509 (t-90) cc_final: 0.7209 (t-170) REVERT: F 191 GLU cc_start: 0.8641 (tm-30) cc_final: 0.7925 (tm-30) REVERT: F 210 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8600 (tp) REVERT: F 220 THR cc_start: 0.9342 (m) cc_final: 0.9008 (m) outliers start: 56 outliers final: 51 residues processed: 216 average time/residue: 0.1525 time to fit residues: 48.7702 Evaluate side-chains 236 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 54 TRP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 54 TRP Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.138250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104273 restraints weight = 12050.375| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.89 r_work: 0.3265 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3174 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= 0.211 Angle : 0.601 12.283 10804 Z= 0.293 Chirality : 0.041 0.202 1232 Planarity : 0.004 0.035 1256 Dihedral : 17.410 88.966 1341 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 7.29 % Allowed : 19.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.29), residues: 892 helix: 1.46 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.90 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 209 HIS 0.001 0.000 HIS E 101 PHE 0.019 0.001 PHE D 215 TYR 0.008 0.001 TYR E 211 ARG 0.005 0.000 ARG F 116 *********************** 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 242 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7339 (ppp) cc_final: 0.7066 (ppp) REVERT: A 22 HIS cc_start: 0.7396 (t-90) cc_final: 0.7113 (t-170) REVERT: A 191 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 210 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8543 (tp) REVERT: A 220 THR cc_start: 0.9356 (m) cc_final: 0.9015 (m) REVERT: D 16 MET cc_start: 0.7402 (ppp) cc_final: 0.7158 (ppp) REVERT: D 22 HIS cc_start: 0.7477 (t-90) cc_final: 0.7174 (t-170) REVERT: D 191 GLU cc_start: 0.8623 (tm-30) cc_final: 0.7866 (tm-30) REVERT: D 220 THR cc_start: 0.9352 (m) cc_final: 0.9005 (m) REVERT: E 22 HIS cc_start: 0.7502 (t-90) cc_final: 0.7162 (t-170) REVERT: E 135 ASP cc_start: 0.8573 (t0) cc_final: 0.8372 (t0) REVERT: E 191 GLU cc_start: 0.8663 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 220 THR cc_start: 0.9338 (m) cc_final: 0.9014 (m) REVERT: F 16 MET cc_start: 0.7362 (ppp) cc_final: 0.7105 (ppp) REVERT: F 22 HIS cc_start: 0.7480 (t-90) cc_final: 0.7185 (t-170) REVERT: F 191 GLU cc_start: 0.8571 (tm-30) cc_final: 0.7801 (tm-30) REVERT: F 210 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8595 (tp) REVERT: F 220 THR cc_start: 0.9330 (m) cc_final: 0.8991 (m) outliers start: 58 outliers final: 50 residues processed: 217 average time/residue: 0.1349 time to fit residues: 43.6727 Evaluate side-chains 236 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 235 VAL 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 65 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.138739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104726 restraints weight = 11934.176| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.92 r_work: 0.3217 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7988 Z= 0.195 Angle : 0.617 17.401 10804 Z= 0.296 Chirality : 0.041 0.187 1232 Planarity : 0.004 0.035 1256 Dihedral : 16.953 87.892 1332 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.66 % Allowed : 21.11 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 892 helix: 1.50 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.82 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 89 HIS 0.000 0.000 HIS F 101 PHE 0.019 0.001 PHE D 215 TYR 0.008 0.001 TYR E 211 ARG 0.004 0.000 ARG D 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 HIS cc_start: 0.7174 (t-90) cc_final: 0.6959 (t-170) REVERT: A 191 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8033 (tm-30) REVERT: A 210 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8420 (tp) REVERT: A 220 THR cc_start: 0.9214 (m) cc_final: 0.8868 (m) REVERT: D 16 MET cc_start: 0.7351 (ppp) cc_final: 0.7134 (ppp) REVERT: D 22 HIS cc_start: 0.7336 (t-90) cc_final: 0.7101 (t-170) REVERT: D 191 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7674 (tm-30) REVERT: D 220 THR cc_start: 0.9260 (m) cc_final: 0.8907 (m) REVERT: E 22 HIS cc_start: 0.7339 (t-90) cc_final: 0.7071 (t-170) REVERT: E 73 MET cc_start: 0.8812 (mtm) cc_final: 0.8478 (mtp) REVERT: E 191 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7766 (tm-30) REVERT: E 220 THR cc_start: 0.9229 (m) cc_final: 0.8900 (m) REVERT: F 22 HIS cc_start: 0.7345 (t-90) cc_final: 0.7117 (t-170) REVERT: F 191 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7686 (tm-30) REVERT: F 210 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8463 (tp) REVERT: F 220 THR cc_start: 0.9220 (m) cc_final: 0.8877 (m) outliers start: 53 outliers final: 50 residues processed: 211 average time/residue: 0.1352 time to fit residues: 42.8168 Evaluate side-chains 235 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 70 GLU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 TRP Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain 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 70 GLU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 108 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.138882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104952 restraints weight = 11841.028| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.91 r_work: 0.3224 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7988 Z= 0.198 Angle : 0.663 19.961 10804 Z= 0.313 Chirality : 0.041 0.161 1232 Planarity : 0.004 0.035 1256 Dihedral : 16.913 87.388 1332 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 6.91 % Allowed : 21.23 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 892 helix: 1.52 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -2.66 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 89 HIS 0.000 0.000 HIS E 101 PHE 0.019 0.001 PHE D 215 TYR 0.008 0.001 TYR E 211 ARG 0.004 0.000 ARG D 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4439.43 seconds wall clock time: 77 minutes 42.98 seconds (4662.98 seconds total)