Starting phenix.real_space_refine on Tue Mar 3 18:15:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tau_10428/03_2026/6tau_10428.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tau_10428/03_2026/6tau_10428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tau_10428/03_2026/6tau_10428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tau_10428/03_2026/6tau_10428.map" model { file = "/net/cci-nas-00/data/ceres_data/6tau_10428/03_2026/6tau_10428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tau_10428/03_2026/6tau_10428.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5172 2.51 5 N 1428 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8148 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "B" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "C" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "D" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "E" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "F" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1358 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Time building chain proxies: 2.01, per 1000 atoms: 0.25 Number of scatterers: 8148 At special positions: 0 Unit cell: (131.86, 63.848, 129.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1524 8.00 N 1428 7.00 C 5172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 208.0 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 44 through 63 removed outlier: 3.700A pdb=" N VAL A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.718A pdb=" N LEU A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.611A pdb=" N ALA A 92 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.785A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.844A pdb=" N ILE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.518A pdb=" N PHE A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.839A pdb=" N GLU A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.615A pdb=" N GLU A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 192 removed outlier: 4.163A pdb=" N LEU A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 63 removed outlier: 3.570A pdb=" N VAL B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.875A pdb=" N LEU B 75 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.515A pdb=" N TRP B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 88 " --> pdb=" O TRP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.965A pdb=" N PHE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.641A pdb=" N ILE B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.592A pdb=" N PHE B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.808A pdb=" N GLU B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.223A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 63 removed outlier: 3.783A pdb=" N VAL C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 4.195A pdb=" N LYS C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'C' and resid 73 through 76 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.988A pdb=" N VAL C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 88 " --> pdb=" O TRP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 107 removed outlier: 3.888A pdb=" N HIS C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.782A pdb=" N ILE C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.790A pdb=" N PHE C 133 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 removed outlier: 4.078A pdb=" N GLU C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 168 removed outlier: 3.696A pdb=" N ARG C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 168 " --> pdb=" O PRO C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 168' Processing helix chain 'C' and resid 177 through 192 removed outlier: 4.003A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 63 removed outlier: 3.700A pdb=" N VAL D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.718A pdb=" N LEU D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 80 through 86 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.611A pdb=" N ALA D 92 " --> pdb=" O ARG D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 107 removed outlier: 3.785A pdb=" N LEU D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 120 removed outlier: 3.845A pdb=" N ILE D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.518A pdb=" N PHE D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.777A pdb=" N PHE D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.614A pdb=" N GLU D 168 " --> pdb=" O PRO D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 4.162A pdb=" N LEU D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 63 removed outlier: 3.570A pdb=" N VAL E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 76 removed outlier: 3.876A pdb=" N LEU E 75 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 88 removed outlier: 3.515A pdb=" N TRP E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY E 87 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL E 88 " --> pdb=" O TRP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 Processing helix chain 'E' and resid 94 through 107 removed outlier: 3.965A pdb=" N PHE E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.641A pdb=" N ILE E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 142 removed outlier: 3.592A pdb=" N PHE E 133 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 162 removed outlier: 3.625A pdb=" N GLU E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 192 removed outlier: 4.222A pdb=" N LEU E 182 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL E 188 " --> pdb=" O ARG E 184 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 63 removed outlier: 3.783A pdb=" N VAL F 48 " --> pdb=" O ASP F 44 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 4.195A pdb=" N LYS F 71 " --> pdb=" O LYS F 67 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 73 through 76 Processing helix chain 'F' and resid 79 through 88 removed outlier: 3.988A pdb=" N VAL F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 87 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL F 88 " --> pdb=" O TRP F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 removed outlier: 3.889A pdb=" N HIS F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.783A pdb=" N ILE F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 142 removed outlier: 3.791A pdb=" N PHE F 133 " --> pdb=" O VAL F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.941A pdb=" N GLU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET F 162 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 168 removed outlier: 3.696A pdb=" N ARG F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU F 168 " --> pdb=" O PRO F 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 163 through 168' Processing helix chain 'F' and resid 177 through 192 removed outlier: 4.004A pdb=" N LEU F 181 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU F 182 " --> pdb=" O PHE F 178 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL F 188 " --> pdb=" O ARG F 184 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 924 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: 1.00 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2673 1.34 - 1.46: 1681 1.46 - 1.58: 3938 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 8328 Sorted by residual: bond pdb=" N MET A 162 " pdb=" CA MET A 162 " ideal model delta sigma weight residual 1.454 1.514 -0.059 1.15e-02 7.56e+03 2.66e+01 bond pdb=" C GLU C 154 " pdb=" O GLU C 154 " ideal model delta sigma weight residual 1.237 1.295 -0.058 1.17e-02 7.31e+03 2.48e+01 bond pdb=" C ILE C 158 " pdb=" O ILE C 158 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.17e-02 7.31e+03 2.03e+01 bond pdb=" N MET F 162 " pdb=" CA MET F 162 " ideal model delta sigma weight residual 1.453 1.511 -0.058 1.31e-02 5.83e+03 1.94e+01 bond pdb=" N MET C 162 " pdb=" CA MET C 162 " ideal model delta sigma weight residual 1.456 1.506 -0.050 1.25e-02 6.40e+03 1.61e+01 ... (remaining 8323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 10812 2.40 - 4.80: 341 4.80 - 7.20: 52 7.20 - 9.59: 7 9.59 - 11.99: 2 Bond angle restraints: 11214 Sorted by residual: angle pdb=" C MET C 162 " pdb=" N GLN C 163 " pdb=" CA GLN C 163 " ideal model delta sigma weight residual 120.60 132.59 -11.99 1.53e+00 4.27e-01 6.14e+01 angle pdb=" C MET E 162 " pdb=" N GLN E 163 " pdb=" CA GLN E 163 " ideal model delta sigma weight residual 120.39 130.35 -9.96 1.39e+00 5.18e-01 5.14e+01 angle pdb=" N PHE D 157 " pdb=" CA PHE D 157 " pdb=" C PHE D 157 " ideal model delta sigma weight residual 111.07 117.01 -5.94 1.07e+00 8.73e-01 3.08e+01 angle pdb=" N MET C 162 " pdb=" CA MET C 162 " pdb=" C MET C 162 " ideal model delta sigma weight residual 110.35 117.56 -7.21 1.36e+00 5.41e-01 2.81e+01 angle pdb=" C MET A 162 " pdb=" N GLN A 163 " pdb=" CA GLN A 163 " ideal model delta sigma weight residual 120.86 128.51 -7.65 1.60e+00 3.91e-01 2.28e+01 ... (remaining 11209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4491 17.72 - 35.44: 449 35.44 - 53.16: 70 53.16 - 70.88: 26 70.88 - 88.60: 16 Dihedral angle restraints: 5052 sinusoidal: 2166 harmonic: 2886 Sorted by residual: dihedral pdb=" CA LYS F 78 " pdb=" C LYS F 78 " pdb=" N SER F 79 " pdb=" CA SER F 79 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N SER C 79 " pdb=" CA SER C 79 " ideal model delta harmonic sigma weight residual 180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA SER C 107 " pdb=" C SER C 107 " pdb=" N PRO C 108 " pdb=" CA PRO C 108 " ideal model delta harmonic sigma weight residual 180.00 -160.70 -19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 937 0.055 - 0.110: 159 0.110 - 0.164: 68 0.164 - 0.219: 17 0.219 - 0.274: 7 Chirality restraints: 1188 Sorted by residual: chirality pdb=" CB THR D 109 " pdb=" CA THR D 109 " pdb=" OG1 THR D 109 " pdb=" CG2 THR D 109 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB THR A 109 " pdb=" CA THR A 109 " pdb=" OG1 THR A 109 " pdb=" CG2 THR A 109 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA THR A 109 " pdb=" N THR A 109 " pdb=" C THR A 109 " pdb=" CB THR A 109 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1185 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 155 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C LEU F 155 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU F 155 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP F 156 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 155 " -0.018 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU D 155 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU D 155 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP D 156 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 163 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO E 164 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.045 5.00e-02 4.00e+02 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 4 2.01 - 2.73: 528 2.73 - 3.45: 10972 3.45 - 4.18: 15381 4.18 - 4.90: 27118 Nonbonded interactions: 54003 Sorted by model distance: nonbonded pdb=" OD1 ASP A 156 " pdb=" NH2 ARG A 172 " model vdw 1.283 3.120 nonbonded pdb=" O ASP A 150 " pdb=" OE2 GLU A 154 " model vdw 1.337 3.040 nonbonded pdb=" O ASP A 150 " pdb=" CD GLU A 154 " model vdw 1.634 3.270 nonbonded pdb=" O ASP A 150 " pdb=" OE1 GLU A 154 " model vdw 1.719 3.040 nonbonded pdb=" O PHE B 157 " pdb=" CD2 LEU B 161 " model vdw 2.090 3.460 ... (remaining 53998 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.550 Find NCS groups from input model: 0.130 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 : 0.006 0.059 8328 Z= 0.399 Angle : 0.992 11.992 11214 Z= 0.647 Chirality : 0.056 0.274 1188 Planarity : 0.009 0.082 1446 Dihedral : 15.437 88.596 3180 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.23 % Allowed : 5.74 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.19), residues: 972 helix: -2.49 (0.17), residues: 512 sheet: None (None), residues: 0 loop : -3.19 (0.20), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.018 0.002 TYR F 126 PHE 0.016 0.002 PHE E 77 TRP 0.014 0.002 TRP B 95 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00590 ( 8328) covalent geometry : angle 0.99204 (11214) hydrogen bonds : bond 0.17490 ( 318) hydrogen bonds : angle 6.18245 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.7822 (tp30) cc_final: 0.7499 (tp30) REVERT: B 50 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6793 (tm-30) REVERT: B 117 MET cc_start: 0.7398 (tpt) cc_final: 0.6139 (mtt) REVERT: B 123 LYS cc_start: 0.8106 (mttt) cc_final: 0.7882 (mtpp) REVERT: C 43 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7970 (mtp85) REVERT: C 90 ARG cc_start: 0.8341 (ptt90) cc_final: 0.8107 (ptt-90) REVERT: E 50 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7231 (tp30) REVERT: E 117 MET cc_start: 0.7716 (tpt) cc_final: 0.6373 (mtt) REVERT: F 168 GLU cc_start: 0.7779 (pp20) cc_final: 0.7480 (pp20) outliers start: 2 outliers final: 1 residues processed: 206 average time/residue: 0.1416 time to fit residues: 35.6499 Evaluate side-chains 158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN B 114 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN E 114 GLN E 163 GLN F 45 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117576 restraints weight = 13065.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120893 restraints weight = 7518.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123261 restraints weight = 4935.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124920 restraints weight = 3528.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126089 restraints weight = 2693.292| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8328 Z= 0.142 Angle : 0.581 9.477 11214 Z= 0.312 Chirality : 0.042 0.188 1188 Planarity : 0.006 0.060 1446 Dihedral : 4.673 22.458 1100 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.13 % Allowed : 12.16 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.23), residues: 972 helix: -0.65 (0.20), residues: 520 sheet: None (None), residues: 0 loop : -2.42 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 43 TYR 0.013 0.002 TYR B 166 PHE 0.016 0.001 PHE A 120 TRP 0.010 0.001 TRP D 95 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8328) covalent geometry : angle 0.58103 (11214) hydrogen bonds : bond 0.04323 ( 318) hydrogen bonds : angle 4.11976 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.210 Fit side-chains REVERT: A 128 GLU cc_start: 0.7652 (tp30) cc_final: 0.7401 (tp30) REVERT: B 50 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7165 (tm-30) REVERT: B 123 LYS cc_start: 0.7975 (mttt) cc_final: 0.7707 (mtpp) REVERT: C 67 LYS cc_start: 0.8353 (tptt) cc_final: 0.8115 (tptt) REVERT: D 162 MET cc_start: 0.6666 (mpp) cc_final: 0.6320 (mmm) outliers start: 10 outliers final: 8 residues processed: 174 average time/residue: 0.1191 time to fit residues: 26.1802 Evaluate side-chains 166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 0.0970 chunk 68 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS B 163 GLN D 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112079 restraints weight = 13214.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115465 restraints weight = 7421.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117815 restraints weight = 4791.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119482 restraints weight = 3383.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120679 restraints weight = 2553.378| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8328 Z= 0.224 Angle : 0.629 8.323 11214 Z= 0.342 Chirality : 0.045 0.196 1188 Planarity : 0.005 0.058 1446 Dihedral : 4.756 25.226 1098 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.48 % Allowed : 14.53 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.24), residues: 972 helix: -0.05 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.37 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 90 TYR 0.023 0.002 TYR B 166 PHE 0.023 0.002 PHE B 120 TRP 0.014 0.002 TRP B 95 HIS 0.008 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 8328) covalent geometry : angle 0.62879 (11214) hydrogen bonds : bond 0.05898 ( 318) hydrogen bonds : angle 4.24985 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.322 Fit side-chains REVERT: A 117 MET cc_start: 0.8252 (tpp) cc_final: 0.7360 (ttp) REVERT: A 128 GLU cc_start: 0.7607 (tp30) cc_final: 0.7386 (tp30) REVERT: A 173 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7156 (p-80) REVERT: B 50 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7212 (tm-30) REVERT: B 117 MET cc_start: 0.7808 (tpp) cc_final: 0.7523 (tpp) REVERT: C 118 GLU cc_start: 0.8469 (tp30) cc_final: 0.7932 (tp30) REVERT: C 180 GLU cc_start: 0.7316 (mp0) cc_final: 0.7059 (mm-30) REVERT: D 91 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6959 (t70) REVERT: D 162 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6605 (mmm) REVERT: D 173 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7454 (p-80) REVERT: E 117 MET cc_start: 0.7779 (tpp) cc_final: 0.7495 (tpp) REVERT: E 174 GLU cc_start: 0.7885 (mp0) cc_final: 0.7308 (mp0) outliers start: 22 outliers final: 11 residues processed: 187 average time/residue: 0.1254 time to fit residues: 29.3581 Evaluate side-chains 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 64 optimal weight: 0.0570 chunk 17 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116482 restraints weight = 13511.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119799 restraints weight = 7705.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122097 restraints weight = 5017.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123737 restraints weight = 3569.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124873 restraints weight = 2711.081| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8328 Z= 0.117 Angle : 0.523 7.527 11214 Z= 0.281 Chirality : 0.040 0.184 1188 Planarity : 0.005 0.055 1446 Dihedral : 4.204 22.908 1098 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.03 % Allowed : 17.34 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.26), residues: 972 helix: 0.62 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.89 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 90 TYR 0.009 0.001 TYR B 166 PHE 0.023 0.001 PHE A 133 TRP 0.011 0.001 TRP B 95 HIS 0.008 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8328) covalent geometry : angle 0.52302 (11214) hydrogen bonds : bond 0.03313 ( 318) hydrogen bonds : angle 3.64696 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.320 Fit side-chains REVERT: A 117 MET cc_start: 0.8002 (tpp) cc_final: 0.7281 (ttp) REVERT: A 173 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7202 (p-80) REVERT: B 117 MET cc_start: 0.7594 (tpp) cc_final: 0.7243 (tpp) REVERT: B 141 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7495 (tt) REVERT: B 162 MET cc_start: 0.7674 (mmm) cc_final: 0.7275 (mmm) REVERT: D 91 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6926 (t70) REVERT: D 117 MET cc_start: 0.8038 (tpp) cc_final: 0.7074 (ttp) REVERT: E 117 MET cc_start: 0.7660 (tpp) cc_final: 0.7264 (tpp) outliers start: 18 outliers final: 8 residues processed: 167 average time/residue: 0.1200 time to fit residues: 25.3437 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 91 optimal weight: 0.0970 chunk 70 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 overall best weight: 2.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112117 restraints weight = 13559.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115288 restraints weight = 7783.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117466 restraints weight = 5112.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119063 restraints weight = 3685.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.120189 restraints weight = 2815.910| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8328 Z= 0.190 Angle : 0.594 9.096 11214 Z= 0.317 Chirality : 0.043 0.180 1188 Planarity : 0.005 0.055 1446 Dihedral : 4.440 25.916 1098 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.04 % Allowed : 17.57 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.26), residues: 972 helix: 0.79 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.90 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 184 TYR 0.015 0.002 TYR C 113 PHE 0.020 0.002 PHE B 120 TRP 0.017 0.001 TRP B 95 HIS 0.009 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8328) covalent geometry : angle 0.59356 (11214) hydrogen bonds : bond 0.05104 ( 318) hydrogen bonds : angle 3.97492 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.321 Fit side-chains REVERT: A 117 MET cc_start: 0.8139 (tpp) cc_final: 0.7378 (ttp) REVERT: A 173 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7207 (p-80) REVERT: B 117 MET cc_start: 0.7672 (tpp) cc_final: 0.7237 (tpp) REVERT: B 123 LYS cc_start: 0.8170 (mttt) cc_final: 0.7940 (mtpp) REVERT: B 141 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7247 (tt) REVERT: B 162 MET cc_start: 0.7637 (mmm) cc_final: 0.7305 (mmm) REVERT: C 67 LYS cc_start: 0.8520 (tptt) cc_final: 0.8221 (tptt) REVERT: C 118 GLU cc_start: 0.8341 (tp30) cc_final: 0.7816 (tp30) REVERT: D 91 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6953 (t70) REVERT: D 117 MET cc_start: 0.8153 (tpp) cc_final: 0.7084 (ttp) REVERT: E 117 MET cc_start: 0.7693 (tpp) cc_final: 0.7266 (tpp) outliers start: 27 outliers final: 15 residues processed: 179 average time/residue: 0.1246 time to fit residues: 28.1855 Evaluate side-chains 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 0.0970 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117883 restraints weight = 13167.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121182 restraints weight = 7532.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123479 restraints weight = 4908.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125028 restraints weight = 3500.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126306 restraints weight = 2677.056| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 : 0.002 0.027 8328 Z= 0.107 Angle : 0.534 8.224 11214 Z= 0.279 Chirality : 0.039 0.181 1188 Planarity : 0.004 0.053 1446 Dihedral : 4.012 24.926 1098 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.14 % Allowed : 19.37 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.26), residues: 972 helix: 1.11 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 184 TYR 0.009 0.001 TYR A 113 PHE 0.013 0.001 PHE A 133 TRP 0.010 0.001 TRP B 95 HIS 0.007 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8328) covalent geometry : angle 0.53392 (11214) hydrogen bonds : bond 0.02695 ( 318) hydrogen bonds : angle 3.48379 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.7849 (tpp) cc_final: 0.7173 (ttp) REVERT: A 173 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.7231 (p-80) REVERT: B 117 MET cc_start: 0.7535 (tpp) cc_final: 0.7078 (tpp) REVERT: B 141 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6716 (tt) REVERT: C 118 GLU cc_start: 0.8285 (tp30) cc_final: 0.7834 (tp30) REVERT: D 91 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6883 (t70) REVERT: D 117 MET cc_start: 0.7986 (tpp) cc_final: 0.7053 (ttp) REVERT: E 117 MET cc_start: 0.7632 (tpp) cc_final: 0.7169 (tpp) outliers start: 19 outliers final: 14 residues processed: 170 average time/residue: 0.1171 time to fit residues: 25.2960 Evaluate side-chains 166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117072 restraints weight = 13452.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120378 restraints weight = 7690.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122675 restraints weight = 5024.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124250 restraints weight = 3581.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125506 restraints weight = 2746.276| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8328 Z= 0.115 Angle : 0.539 9.295 11214 Z= 0.279 Chirality : 0.040 0.236 1188 Planarity : 0.004 0.053 1446 Dihedral : 3.936 24.772 1098 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.48 % Allowed : 19.93 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 972 helix: 1.29 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.46 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 184 TYR 0.009 0.001 TYR C 113 PHE 0.013 0.001 PHE A 133 TRP 0.009 0.001 TRP B 95 HIS 0.008 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8328) covalent geometry : angle 0.53881 (11214) hydrogen bonds : bond 0.03090 ( 318) hydrogen bonds : angle 3.43605 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.310 Fit side-chains REVERT: A 117 MET cc_start: 0.7855 (tpp) cc_final: 0.7166 (ttp) REVERT: A 173 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7278 (p-80) REVERT: B 117 MET cc_start: 0.7584 (tpp) cc_final: 0.7138 (tpp) REVERT: B 121 GLU cc_start: 0.8606 (tp30) cc_final: 0.8348 (tp30) REVERT: B 161 LEU cc_start: 0.8047 (mm) cc_final: 0.7758 (mm) REVERT: B 174 GLU cc_start: 0.7809 (mp0) cc_final: 0.7410 (pm20) REVERT: D 91 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6932 (t70) REVERT: D 117 MET cc_start: 0.7987 (tpp) cc_final: 0.7003 (ttp) REVERT: E 117 MET cc_start: 0.7577 (tpp) cc_final: 0.7128 (tpp) REVERT: E 162 MET cc_start: 0.7652 (mmm) cc_final: 0.7414 (mmm) REVERT: E 174 GLU cc_start: 0.7798 (mp0) cc_final: 0.7273 (pm20) outliers start: 22 outliers final: 14 residues processed: 170 average time/residue: 0.1246 time to fit residues: 26.4520 Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 21 optimal weight: 0.0010 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.134680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119051 restraints weight = 13200.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122399 restraints weight = 7527.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124685 restraints weight = 4913.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.126329 restraints weight = 3506.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127513 restraints weight = 2667.811| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8328 Z= 0.105 Angle : 0.538 9.434 11214 Z= 0.275 Chirality : 0.039 0.218 1188 Planarity : 0.004 0.052 1446 Dihedral : 3.746 23.755 1098 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.14 % Allowed : 20.16 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.27), residues: 972 helix: 1.47 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.33 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 43 TYR 0.009 0.001 TYR A 113 PHE 0.012 0.001 PHE A 133 TRP 0.008 0.001 TRP B 95 HIS 0.008 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8328) covalent geometry : angle 0.53817 (11214) hydrogen bonds : bond 0.02530 ( 318) hydrogen bonds : angle 3.29920 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.313 Fit side-chains REVERT: A 117 MET cc_start: 0.7858 (tpp) cc_final: 0.7173 (ttp) REVERT: A 173 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7280 (p-80) REVERT: B 89 ARG cc_start: 0.8035 (ttt180) cc_final: 0.7672 (ttm-80) REVERT: B 117 MET cc_start: 0.7569 (tpp) cc_final: 0.7134 (tpp) REVERT: B 121 GLU cc_start: 0.8562 (tp30) cc_final: 0.8283 (tp30) REVERT: D 91 ASP cc_start: 0.7227 (OUTLIER) cc_final: 0.6848 (t70) REVERT: D 117 MET cc_start: 0.7964 (tpp) cc_final: 0.7018 (ttp) REVERT: E 117 MET cc_start: 0.7543 (tpp) cc_final: 0.7077 (tpp) outliers start: 19 outliers final: 13 residues processed: 170 average time/residue: 0.1244 time to fit residues: 26.6686 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118708 restraints weight = 13279.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122017 restraints weight = 7591.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124226 restraints weight = 4959.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125935 restraints weight = 3569.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127151 restraints weight = 2720.907| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8328 Z= 0.109 Angle : 0.561 10.687 11214 Z= 0.283 Chirality : 0.040 0.239 1188 Planarity : 0.004 0.051 1446 Dihedral : 3.794 30.094 1098 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.36 % Allowed : 20.61 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.27), residues: 972 helix: 1.56 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.19 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 184 TYR 0.009 0.001 TYR A 113 PHE 0.036 0.001 PHE E 39 TRP 0.008 0.001 TRP B 95 HIS 0.008 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8328) covalent geometry : angle 0.56146 (11214) hydrogen bonds : bond 0.02714 ( 318) hydrogen bonds : angle 3.27804 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.258 Fit side-chains REVERT: A 117 MET cc_start: 0.7885 (tpp) cc_final: 0.7165 (ttp) REVERT: A 173 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7308 (p-80) REVERT: B 117 MET cc_start: 0.7549 (tpp) cc_final: 0.7098 (tpp) REVERT: B 121 GLU cc_start: 0.8542 (tp30) cc_final: 0.8269 (tp30) REVERT: B 174 GLU cc_start: 0.7558 (mp0) cc_final: 0.7230 (pm20) REVERT: D 91 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6758 (t70) REVERT: D 117 MET cc_start: 0.7949 (tpp) cc_final: 0.7004 (ttp) REVERT: E 117 MET cc_start: 0.7539 (tpp) cc_final: 0.7051 (tpp) REVERT: E 174 GLU cc_start: 0.7265 (mp0) cc_final: 0.6823 (pm20) outliers start: 21 outliers final: 15 residues processed: 166 average time/residue: 0.1235 time to fit residues: 25.6508 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116497 restraints weight = 13164.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119720 restraints weight = 7553.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121981 restraints weight = 4957.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123592 restraints weight = 3556.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124539 restraints weight = 2728.133| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8328 Z= 0.133 Angle : 0.581 10.163 11214 Z= 0.296 Chirality : 0.042 0.249 1188 Planarity : 0.004 0.051 1446 Dihedral : 3.943 28.945 1098 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.36 % Allowed : 20.95 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 972 helix: 1.56 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.18 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 184 TYR 0.011 0.001 TYR C 113 PHE 0.030 0.001 PHE E 39 TRP 0.011 0.001 TRP B 95 HIS 0.008 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8328) covalent geometry : angle 0.58109 (11214) hydrogen bonds : bond 0.03556 ( 318) hydrogen bonds : angle 3.37715 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.240 Fit side-chains REVERT: A 117 MET cc_start: 0.7918 (tpp) cc_final: 0.7153 (ttp) REVERT: A 173 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.7385 (p-80) REVERT: B 117 MET cc_start: 0.7608 (tpp) cc_final: 0.7146 (tpp) REVERT: B 121 GLU cc_start: 0.8572 (tp30) cc_final: 0.8301 (tp30) REVERT: B 174 GLU cc_start: 0.7702 (mp0) cc_final: 0.7283 (pm20) REVERT: C 118 GLU cc_start: 0.8276 (tp30) cc_final: 0.7711 (tp30) REVERT: C 128 GLU cc_start: 0.7781 (tp30) cc_final: 0.7041 (tt0) REVERT: D 91 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6782 (t70) REVERT: D 117 MET cc_start: 0.8026 (tpp) cc_final: 0.7023 (ttp) REVERT: E 117 MET cc_start: 0.7571 (tpp) cc_final: 0.7184 (tpp) REVERT: E 174 GLU cc_start: 0.7532 (mp0) cc_final: 0.6841 (pm20) REVERT: F 128 GLU cc_start: 0.7996 (tp30) cc_final: 0.7100 (tt0) outliers start: 21 outliers final: 18 residues processed: 164 average time/residue: 0.1285 time to fit residues: 26.3399 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 chunk 64 optimal weight: 0.0020 chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.4926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119733 restraints weight = 13134.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123038 restraints weight = 7529.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125339 restraints weight = 4931.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126990 restraints weight = 3526.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128136 restraints weight = 2693.067| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8328 Z= 0.106 Angle : 0.561 9.779 11214 Z= 0.283 Chirality : 0.040 0.245 1188 Planarity : 0.004 0.050 1446 Dihedral : 3.766 28.578 1098 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.36 % Allowed : 20.72 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 972 helix: 1.68 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.07 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 184 TYR 0.009 0.001 TYR A 113 PHE 0.027 0.001 PHE E 39 TRP 0.009 0.001 TRP B 95 HIS 0.008 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8328) covalent geometry : angle 0.56070 (11214) hydrogen bonds : bond 0.02403 ( 318) hydrogen bonds : angle 3.26107 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.13 seconds wall clock time: 22 minutes 19.83 seconds (1339.83 seconds total)