Starting phenix.real_space_refine on Wed Mar 12 13:11:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tau_10428/03_2025/6tau_10428.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tau_10428/03_2025/6tau_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_2025/6tau_10428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tau_10428/03_2025/6tau_10428.map" model { file = "/net/cci-nas-00/data/ceres_data/6tau_10428/03_2025/6tau_10428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tau_10428/03_2025/6tau_10428.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.40, per 1000 atoms: 0.66 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: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.75 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: 1.77 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.530 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- 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= 0.379 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (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 TRP 0.014 0.002 TRP B 95 HIS 0.005 0.001 HIS E 173 PHE 0.016 0.002 PHE E 77 TYR 0.018 0.002 TYR F 126 ARG 0.002 0.000 ARG E 148 *********************** 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 : 1.002 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: 0.3079 time to fit residues: 77.6251 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 : 0.894 ------------------------------------------------------------------------------- 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 81 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 124 GLN B 114 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN E 114 GLN E 163 GLN ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112954 restraints weight = 13223.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116144 restraints weight = 7650.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118406 restraints weight = 5021.960| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8328 Z= 0.320 Angle : 0.647 9.486 11214 Z= 0.350 Chirality : 0.045 0.187 1188 Planarity : 0.006 0.064 1446 Dihedral : 4.975 23.671 1100 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.91 % Allowed : 12.61 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.23), residues: 972 helix: -0.76 (0.20), residues: 532 sheet: None (None), residues: 0 loop : -2.62 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 95 HIS 0.005 0.001 HIS B 173 PHE 0.025 0.002 PHE B 120 TYR 0.022 0.002 TYR B 166 ARG 0.006 0.001 ARG D 184 *********************** 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 198 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.937 Fit side-chains REVERT: A 128 GLU cc_start: 0.7544 (tp30) cc_final: 0.7323 (tp30) REVERT: C 90 ARG cc_start: 0.8365 (ptt90) cc_final: 0.8113 (ptt-90) REVERT: C 118 GLU cc_start: 0.8351 (tp30) cc_final: 0.7812 (tp30) REVERT: D 162 MET cc_start: 0.6916 (mpp) cc_final: 0.6491 (mmm) REVERT: F 50 GLU cc_start: 0.7784 (tt0) cc_final: 0.7574 (tt0) outliers start: 17 outliers final: 10 residues processed: 190 average time/residue: 0.2578 time to fit residues: 61.8407 Evaluate side-chains 171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** B 163 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** 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 = 0.3630 r_free = 0.3630 target = 0.133290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116755 restraints weight = 13282.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120297 restraints weight = 7428.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122728 restraints weight = 4764.333| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8328 Z= 0.194 Angle : 0.546 7.758 11214 Z= 0.294 Chirality : 0.041 0.182 1188 Planarity : 0.005 0.058 1446 Dihedral : 4.373 24.506 1098 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.36 % Allowed : 14.86 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 972 helix: 0.11 (0.21), residues: 532 sheet: None (None), residues: 0 loop : -2.33 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 95 HIS 0.007 0.001 HIS B 173 PHE 0.021 0.001 PHE A 133 TYR 0.012 0.001 TYR B 166 ARG 0.005 0.000 ARG C 43 *********************** 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 182 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.039 Fit side-chains REVERT: A 117 MET cc_start: 0.8004 (tpp) cc_final: 0.7138 (ttp) REVERT: B 117 MET cc_start: 0.7614 (tpp) cc_final: 0.7338 (tpp) REVERT: B 162 MET cc_start: 0.7794 (mmm) cc_final: 0.7385 (mmt) REVERT: C 43 ARG cc_start: 0.8675 (mtp85) cc_final: 0.8423 (mtp85) REVERT: C 90 ARG cc_start: 0.8343 (ptt90) cc_final: 0.8095 (ptt-90) REVERT: D 117 MET cc_start: 0.8011 (tpp) cc_final: 0.6932 (ttp) REVERT: D 162 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6269 (mmm) REVERT: D 173 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7423 (p-80) REVERT: E 117 MET cc_start: 0.7501 (tpp) cc_final: 0.7250 (tpp) REVERT: E 174 GLU cc_start: 0.7969 (mp0) cc_final: 0.7290 (pm20) outliers start: 21 outliers final: 12 residues processed: 171 average time/residue: 0.2816 time to fit residues: 60.5552 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 88 VAL 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 D residue 153 THR Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 173 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 45 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117794 restraints weight = 13191.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.121124 restraints weight = 7562.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123421 restraints weight = 4945.343| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2680 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= 0.161 Angle : 0.514 8.577 11214 Z= 0.273 Chirality : 0.039 0.182 1188 Planarity : 0.004 0.054 1446 Dihedral : 4.015 22.692 1098 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.14 % Allowed : 16.10 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 972 helix: 0.60 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 95 HIS 0.008 0.001 HIS B 173 PHE 0.015 0.001 PHE A 133 TYR 0.009 0.001 TYR D 113 ARG 0.007 0.000 ARG D 184 *********************** 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 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.910 Fit side-chains REVERT: A 117 MET cc_start: 0.7873 (tpp) cc_final: 0.7097 (ttp) REVERT: B 117 MET cc_start: 0.7594 (tpp) cc_final: 0.7226 (tpp) REVERT: C 43 ARG cc_start: 0.8628 (mtp85) cc_final: 0.8380 (mtp85) REVERT: C 67 LYS cc_start: 0.8657 (tptt) cc_final: 0.8449 (tptt) REVERT: C 90 ARG cc_start: 0.8268 (ptt90) cc_final: 0.8052 (ptt-90) REVERT: D 52 ILE cc_start: 0.8034 (tt) cc_final: 0.7775 (tt) REVERT: D 117 MET cc_start: 0.8005 (tpp) cc_final: 0.7016 (ttp) REVERT: D 173 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7395 (p-80) REVERT: E 117 MET cc_start: 0.7512 (tpp) cc_final: 0.7154 (tpp) outliers start: 19 outliers final: 11 residues processed: 168 average time/residue: 0.2757 time to fit residues: 58.2068 Evaluate side-chains 161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 129 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 173 HIS 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 72 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 94 optimal weight: 0.1980 chunk 54 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.133458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117927 restraints weight = 13029.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121250 restraints weight = 7441.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123564 restraints weight = 4855.611| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2898 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= 0.162 Angle : 0.522 9.451 11214 Z= 0.271 Chirality : 0.039 0.178 1188 Planarity : 0.004 0.051 1446 Dihedral : 3.908 24.707 1098 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.27 % Allowed : 16.33 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 972 helix: 0.91 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.83 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 95 HIS 0.009 0.001 HIS A 173 PHE 0.012 0.001 PHE A 133 TYR 0.009 0.001 TYR D 113 ARG 0.010 0.000 ARG D 184 *********************** 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: 29 poor density : 158 time to evaluate : 0.930 Fit side-chains REVERT: A 117 MET cc_start: 0.7892 (tpp) cc_final: 0.7131 (ttp) REVERT: B 117 MET cc_start: 0.7574 (tpp) cc_final: 0.7126 (tpp) REVERT: B 174 GLU cc_start: 0.7879 (mp0) cc_final: 0.7619 (pm20) REVERT: C 67 LYS cc_start: 0.8647 (tptt) cc_final: 0.8317 (tptt) REVERT: C 118 GLU cc_start: 0.8244 (tp30) cc_final: 0.7803 (tp30) REVERT: D 91 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6762 (t70) REVERT: D 117 MET cc_start: 0.8020 (tpp) cc_final: 0.7045 (ttp) REVERT: D 173 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7731 (p-80) REVERT: E 117 MET cc_start: 0.7545 (tpp) cc_final: 0.7110 (tpp) REVERT: E 174 GLU cc_start: 0.7924 (mp0) cc_final: 0.7614 (mp0) outliers start: 29 outliers final: 15 residues processed: 176 average time/residue: 0.2723 time to fit residues: 60.0103 Evaluate side-chains 161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B 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 D residue 153 THR 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 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 24 optimal weight: 0.0060 chunk 87 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.134972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119479 restraints weight = 13070.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122855 restraints weight = 7465.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125070 restraints weight = 4850.043| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3063 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= 0.154 Angle : 0.538 8.932 11214 Z= 0.276 Chirality : 0.040 0.230 1188 Planarity : 0.004 0.049 1446 Dihedral : 3.802 24.182 1098 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.59 % Allowed : 18.36 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 972 helix: 1.14 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.67 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.009 0.001 HIS A 173 PHE 0.011 0.001 PHE A 133 TYR 0.009 0.001 TYR D 113 ARG 0.011 0.000 ARG D 184 *********************** 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 172 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.013 Fit side-chains REVERT: A 117 MET cc_start: 0.7882 (tpp) cc_final: 0.7109 (ttp) REVERT: B 117 MET cc_start: 0.7542 (tpp) cc_final: 0.7128 (tpp) REVERT: C 67 LYS cc_start: 0.8564 (tptt) cc_final: 0.8257 (tptt) REVERT: C 118 GLU cc_start: 0.8204 (tp30) cc_final: 0.7791 (tp30) REVERT: D 91 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6722 (t70) REVERT: D 117 MET cc_start: 0.7955 (tpp) cc_final: 0.6969 (ttp) REVERT: E 117 MET cc_start: 0.7489 (tpp) cc_final: 0.7051 (tpp) REVERT: E 162 MET cc_start: 0.7570 (mmm) cc_final: 0.7363 (mmm) REVERT: E 174 GLU cc_start: 0.7860 (mp0) cc_final: 0.7221 (pm20) outliers start: 23 outliers final: 17 residues processed: 164 average time/residue: 0.2970 time to fit residues: 61.8022 Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B 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 D residue 153 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL 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 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 22 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.134658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118876 restraints weight = 13127.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122248 restraints weight = 7539.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124605 restraints weight = 4936.384| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8328 Z= 0.162 Angle : 0.528 7.055 11214 Z= 0.273 Chirality : 0.040 0.205 1188 Planarity : 0.004 0.049 1446 Dihedral : 3.736 23.949 1098 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.59 % Allowed : 17.91 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 972 helix: 1.28 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.52 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 95 HIS 0.009 0.001 HIS A 173 PHE 0.010 0.001 PHE A 133 TYR 0.009 0.001 TYR D 113 ARG 0.012 0.000 ARG D 184 *********************** 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 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.959 Fit side-chains REVERT: A 117 MET cc_start: 0.7911 (tpp) cc_final: 0.7145 (ttp) REVERT: B 117 MET cc_start: 0.7570 (tpp) cc_final: 0.7131 (tpp) REVERT: C 118 GLU cc_start: 0.8195 (tp30) cc_final: 0.7786 (tp30) REVERT: D 91 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6722 (t70) REVERT: D 117 MET cc_start: 0.7982 (tpp) cc_final: 0.6956 (ttp) REVERT: E 117 MET cc_start: 0.7516 (tpp) cc_final: 0.7074 (tpp) outliers start: 23 outliers final: 19 residues processed: 167 average time/residue: 0.2840 time to fit residues: 59.6582 Evaluate side-chains 168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 184 ARG 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 D residue 153 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115828 restraints weight = 13401.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119147 restraints weight = 7714.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121461 restraints weight = 5044.893| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8328 Z= 0.227 Angle : 0.583 10.662 11214 Z= 0.300 Chirality : 0.042 0.226 1188 Planarity : 0.004 0.049 1446 Dihedral : 4.007 26.447 1098 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.36 % Allowed : 18.81 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 972 helix: 1.29 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 95 HIS 0.009 0.001 HIS A 173 PHE 0.012 0.001 PHE B 120 TYR 0.012 0.001 TYR C 113 ARG 0.007 0.000 ARG D 184 *********************** 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 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.941 Fit side-chains REVERT: A 117 MET cc_start: 0.7962 (tpp) cc_final: 0.7188 (ttp) REVERT: B 89 ARG cc_start: 0.8027 (ttt180) cc_final: 0.7694 (ttm-80) REVERT: B 95 TRP cc_start: 0.7545 (t-100) cc_final: 0.7243 (t-100) REVERT: B 117 MET cc_start: 0.7629 (tpp) cc_final: 0.7163 (tpp) REVERT: C 118 GLU cc_start: 0.8258 (tp30) cc_final: 0.7707 (tp30) REVERT: D 117 MET cc_start: 0.8043 (tpp) cc_final: 0.6965 (ttp) REVERT: E 117 MET cc_start: 0.7608 (tpp) cc_final: 0.7164 (tpp) REVERT: E 162 MET cc_start: 0.7715 (mmm) cc_final: 0.7453 (mmm) REVERT: F 178 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7892 (t80) outliers start: 21 outliers final: 16 residues processed: 166 average time/residue: 0.2977 time to fit residues: 62.6335 Evaluate side-chains 162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 155 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 153 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL 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 Chi-restraints excluded: chain F residue 178 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 21 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 105 HIS ** 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 = 0.3640 r_free = 0.3640 target = 0.132562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116509 restraints weight = 13461.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.119877 restraints weight = 7702.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122233 restraints weight = 5036.353| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8328 Z= 0.182 Angle : 0.550 8.996 11214 Z= 0.285 Chirality : 0.041 0.207 1188 Planarity : 0.004 0.050 1446 Dihedral : 3.896 26.828 1098 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.91 % Allowed : 19.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.27), residues: 972 helix: 1.39 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.010 0.001 HIS A 173 PHE 0.009 0.001 PHE B 120 TYR 0.009 0.001 TYR C 113 ARG 0.007 0.000 ARG D 184 *********************** 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 169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.013 Fit side-chains REVERT: A 117 MET cc_start: 0.7909 (tpp) cc_final: 0.7037 (ttp) REVERT: B 89 ARG cc_start: 0.8013 (ttt180) cc_final: 0.7668 (ttm-80) REVERT: B 117 MET cc_start: 0.7603 (tpp) cc_final: 0.7149 (tpp) REVERT: C 118 GLU cc_start: 0.8292 (tp30) cc_final: 0.7749 (tp30) REVERT: D 117 MET cc_start: 0.7987 (tpp) cc_final: 0.6949 (ttp) REVERT: E 117 MET cc_start: 0.7579 (tpp) cc_final: 0.7143 (tpp) REVERT: F 90 ARG cc_start: 0.8200 (ptt90) cc_final: 0.7821 (ptt90) REVERT: F 178 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7759 (t80) outliers start: 17 outliers final: 15 residues processed: 163 average time/residue: 0.2815 time to fit residues: 57.5133 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B 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 153 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL 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 Chi-restraints excluded: chain F residue 178 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.134783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118730 restraints weight = 13106.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122096 restraints weight = 7550.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124424 restraints weight = 4958.771| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8328 Z= 0.163 Angle : 0.560 11.303 11214 Z= 0.284 Chirality : 0.040 0.210 1188 Planarity : 0.004 0.050 1446 Dihedral : 3.708 26.554 1098 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.91 % Allowed : 19.48 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 972 helix: 1.64 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.05 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 85 HIS 0.010 0.001 HIS A 173 PHE 0.008 0.001 PHE A 133 TYR 0.010 0.001 TYR D 113 ARG 0.008 0.000 ARG D 184 ********************** 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: 17 poor density : 155 time to evaluate : 1.013 Fit side-chains REVERT: A 117 MET cc_start: 0.7871 (tpp) cc_final: 0.7072 (ttp) REVERT: B 89 ARG cc_start: 0.8024 (ttt180) cc_final: 0.7675 (ttm-80) REVERT: B 117 MET cc_start: 0.7554 (tpp) cc_final: 0.7108 (tpp) REVERT: D 117 MET cc_start: 0.7978 (tpp) cc_final: 0.7049 (ttp) REVERT: E 117 MET cc_start: 0.7540 (tpp) cc_final: 0.7117 (tpp) REVERT: F 90 ARG cc_start: 0.8158 (ptt90) cc_final: 0.7786 (ptt90) REVERT: F 127 ASP cc_start: 0.8513 (p0) cc_final: 0.8263 (p0) REVERT: F 178 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7660 (t80) outliers start: 17 outliers final: 15 residues processed: 166 average time/residue: 0.2793 time to fit residues: 58.0698 Evaluate side-chains 166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B 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 153 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 VAL 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 Chi-restraints excluded: chain F residue 178 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114025 restraints weight = 13617.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117342 restraints weight = 7784.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119624 restraints weight = 5086.792| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8328 Z= 0.259 Angle : 0.591 10.645 11214 Z= 0.308 Chirality : 0.043 0.265 1188 Planarity : 0.004 0.048 1446 Dihedral : 4.067 27.206 1098 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.25 % Allowed : 19.71 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 972 helix: 1.43 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.35 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 95 HIS 0.009 0.001 HIS A 173 PHE 0.041 0.002 PHE E 39 TYR 0.013 0.001 TYR F 166 ARG 0.009 0.000 ARG D 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.10 seconds wall clock time: 43 minutes 57.85 seconds (2637.85 seconds total)