Starting phenix.real_space_refine on Wed Mar 4 01:45:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ykr_10830/03_2026/6ykr_10830.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ykr_10830/03_2026/6ykr_10830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ykr_10830/03_2026/6ykr_10830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ykr_10830/03_2026/6ykr_10830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ykr_10830/03_2026/6ykr_10830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ykr_10830/03_2026/6ykr_10830.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 70 5.16 5 C 6592 2.51 5 N 1651 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 10189 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "C" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "D" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "E" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "F" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 203 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 210 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.66, per 1000 atoms: 0.26 Number of scatterers: 10189 At special positions: 0 Unit cell: (92.352, 110.656, 104, 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 70 16.00 O 1876 8.00 N 1651 7.00 C 6592 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: 0.74 Conformation dependent library (CDL) restraints added in 505.7 milliseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.658A pdb=" N MET A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.516A pdb=" N LEU A 22 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.617A pdb=" N VAL A 30 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 31 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.841A pdb=" N ILE A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.524A pdb=" N ALA A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.810A pdb=" N LYS A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.546A pdb=" N GLN A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.869A pdb=" N SER A 98 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.525A pdb=" N ASP A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 137 through 160 removed outlier: 3.713A pdb=" N ALA A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 4.050A pdb=" N LEU A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.572A pdb=" N LEU A 169 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 170 " --> pdb=" O LEU A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 170' Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.610A pdb=" N ALA A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 229 removed outlier: 3.986A pdb=" N ASP A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.643A pdb=" N ALA A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.572A pdb=" N ALA B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.882A pdb=" N VAL B 30 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.735A pdb=" N TYR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.567A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.737A pdb=" N ALA B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 removed outlier: 3.637A pdb=" N GLU B 97 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER B 98 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 100 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 3.608A pdb=" N ASP B 117 " --> pdb=" O MET B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 162 removed outlier: 3.608A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.652A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 184 removed outlier: 3.607A pdb=" N MET B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 197 removed outlier: 3.731A pdb=" N VAL B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 229 removed outlier: 3.865A pdb=" N ASP B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 4.088A pdb=" N ALA B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'C' and resid 2 through 24 removed outlier: 3.712A pdb=" N ALA C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.879A pdb=" N VAL C 30 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 31 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 39 through 47 removed outlier: 3.507A pdb=" N ALA C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.662A pdb=" N LYS C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.539A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.584A pdb=" N ALA C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.530A pdb=" N LEU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 97 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.570A pdb=" N ASP C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 removed outlier: 3.729A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 171 removed outlier: 4.194A pdb=" N TRP C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 153 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Proline residue: C 154 - end of helix removed outlier: 3.804A pdb=" N LEU C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 167 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 197 removed outlier: 4.047A pdb=" N ALA C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 229 removed outlier: 3.703A pdb=" N ASP C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'D' and resid 2 through 24 removed outlier: 3.569A pdb=" N MET D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP D 20 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.696A pdb=" N LYS D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.558A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 91 removed outlier: 3.501A pdb=" N ALA D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 99 removed outlier: 3.653A pdb=" N ALA D 95 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU D 97 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER D 98 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 removed outlier: 3.640A pdb=" N ASP D 117 " --> pdb=" O MET D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 170 removed outlier: 3.871A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TRP D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Proline residue: D 154 - end of helix removed outlier: 3.683A pdb=" N LEU D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY D 164 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 167 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 186 removed outlier: 3.761A pdb=" N ALA D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.879A pdb=" N VAL D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 229 removed outlier: 3.873A pdb=" N ASP D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU D 214 " --> pdb=" O ASN D 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.587A pdb=" N ALA D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 22 removed outlier: 3.539A pdb=" N MET E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 38 Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.516A pdb=" N ALA E 44 " --> pdb=" O MET E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 3.595A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.576A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 91 removed outlier: 3.675A pdb=" N ALA E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 removed outlier: 3.607A pdb=" N LEU E 96 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU E 97 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 removed outlier: 3.528A pdb=" N ASN E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP E 117 " --> pdb=" O MET E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 171 removed outlier: 3.571A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE E 130 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TRP E 146 " --> pdb=" O CYS E 142 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N CYS E 153 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Proline residue: E 154 - end of helix Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.722A pdb=" N ALA E 180 " --> pdb=" O GLN E 176 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 195 Processing helix chain 'E' and resid 199 through 229 removed outlier: 3.661A pdb=" N ASP E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 214 " --> pdb=" O ASN E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.690A pdb=" N ALA E 239 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'F' and resid 16 through 39 removed outlier: 3.527A pdb=" N ASN F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 32 removed outlier: 3.844A pdb=" N ASN G 22 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE G 23 " --> pdb=" O PRO G 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 40 644 hydrogen bonds defined for protein. 1893 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: 1.46 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2965 1.34 - 1.45: 1429 1.45 - 1.57: 5853 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 10372 Sorted by residual: bond pdb=" C MET A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.12e+00 bond pdb=" C MET C 40 " pdb=" N PRO C 41 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.59e+00 bond pdb=" CA ILE A 31 " pdb=" CB ILE A 31 " ideal model delta sigma weight residual 1.528 1.547 -0.020 1.34e-02 5.57e+03 2.12e+00 bond pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" CA VAL G 18 " pdb=" C VAL G 18 " ideal model delta sigma weight residual 1.524 1.539 -0.014 1.05e-02 9.07e+03 1.86e+00 ... (remaining 10367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 13757 2.53 - 5.07: 198 5.07 - 7.60: 48 7.60 - 10.13: 9 10.13 - 12.67: 2 Bond angle restraints: 14014 Sorted by residual: angle pdb=" CA LEU B 171 " pdb=" CB LEU B 171 " pdb=" CG LEU B 171 " ideal model delta sigma weight residual 116.30 128.97 -12.67 3.50e+00 8.16e-02 1.31e+01 angle pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " pdb=" CD2 LEU A 158 " ideal model delta sigma weight residual 110.70 100.74 9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CG1 ILE D 38 " pdb=" CB ILE D 38 " pdb=" CG2 ILE D 38 " ideal model delta sigma weight residual 110.70 101.07 9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA LEU E 171 " pdb=" CB LEU E 171 " pdb=" CG LEU E 171 " ideal model delta sigma weight residual 116.30 127.34 -11.04 3.50e+00 8.16e-02 9.95e+00 angle pdb=" CA VAL G 18 " pdb=" CB VAL G 18 " pdb=" CG1 VAL G 18 " ideal model delta sigma weight residual 110.40 115.48 -5.08 1.70e+00 3.46e-01 8.93e+00 ... (remaining 14009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.22: 5897 14.22 - 28.44: 233 28.44 - 42.65: 79 42.65 - 56.87: 7 56.87 - 71.09: 2 Dihedral angle restraints: 6218 sinusoidal: 2425 harmonic: 3793 Sorted by residual: dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N PHE B 200 " pdb=" CA PHE B 200 " ideal model delta harmonic sigma weight residual 180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU A 199 " pdb=" C LEU A 199 " pdb=" N PHE A 200 " pdb=" CA PHE A 200 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA LEU E 199 " pdb=" C LEU E 199 " pdb=" N PHE E 200 " pdb=" CA PHE E 200 " ideal model delta harmonic sigma weight residual 180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 6215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1186 0.055 - 0.109: 404 0.109 - 0.164: 37 0.164 - 0.218: 11 0.218 - 0.273: 2 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CB VAL G 18 " pdb=" CA VAL G 18 " pdb=" CG1 VAL G 18 " pdb=" CG2 VAL G 18 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE A 38 " pdb=" CA ILE A 38 " pdb=" CG1 ILE A 38 " pdb=" CG2 ILE A 38 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU A 158 " pdb=" CB LEU A 158 " pdb=" CD1 LEU A 158 " pdb=" CD2 LEU A 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1637 not shown) Planarity restraints: 1763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 149 " 0.024 2.00e-02 2.50e+03 2.43e-02 1.03e+01 pdb=" CG PHE C 149 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 149 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 149 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 149 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 149 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE C 149 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 149 " 0.021 2.00e-02 2.50e+03 2.19e-02 8.37e+00 pdb=" CG PHE B 149 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B 149 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 149 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 149 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 149 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 149 " -0.020 2.00e-02 2.50e+03 2.17e-02 8.25e+00 pdb=" CG PHE D 149 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE D 149 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE D 149 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE D 149 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE D 149 " -0.001 2.00e-02 2.50e+03 ... (remaining 1760 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3191 2.83 - 3.35: 9492 3.35 - 3.87: 16338 3.87 - 4.38: 21556 4.38 - 4.90: 34364 Nonbonded interactions: 84941 Sorted by model distance: nonbonded pdb=" OG SER B 246 " pdb=" OD1 ASP B 248 " model vdw 2.314 3.040 nonbonded pdb=" OG SER D 246 " pdb=" OD1 ASP D 248 " model vdw 2.329 3.040 nonbonded pdb=" OG SER E 246 " pdb=" OD1 ASP E 248 " model vdw 2.345 3.040 nonbonded pdb=" OG SER A 246 " pdb=" OD1 ASP A 248 " model vdw 2.361 3.040 nonbonded pdb=" OD2 ASP B 20 " pdb=" O HOH B 301 " model vdw 2.378 3.040 ... (remaining 84936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 15 through 39) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.140 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:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.004 0.061 10372 Z= 0.187 Angle : 0.839 12.668 14014 Z= 0.429 Chirality : 0.051 0.273 1640 Planarity : 0.007 0.063 1763 Dihedral : 9.413 71.088 3766 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -6.35 (0.13), residues: 1312 helix: -4.43 (0.07), residues: 1028 sheet: None (None), residues: 0 loop : -1.88 (0.29), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 89 TYR 0.012 0.003 TYR A 197 PHE 0.055 0.003 PHE C 149 TRP 0.017 0.002 TRP B 203 HIS 0.006 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00448 (10372) covalent geometry : angle 0.83946 (14014) hydrogen bonds : bond 0.30038 ( 644) hydrogen bonds : angle 11.62447 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.363 Fit side-chains REVERT: A 83 GLU cc_start: 0.7394 (tt0) cc_final: 0.7159 (mt-10) REVERT: A 140 LYS cc_start: 0.8163 (ttmp) cc_final: 0.7857 (ttpp) REVERT: A 223 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6898 (mm-30) REVERT: B 48 MET cc_start: 0.7797 (ttm) cc_final: 0.7588 (ttt) REVERT: B 62 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7204 (mt-10) REVERT: B 136 GLU cc_start: 0.7684 (tt0) cc_final: 0.7444 (tt0) REVERT: B 145 TYR cc_start: 0.9129 (t80) cc_final: 0.8820 (t80) REVERT: B 156 MET cc_start: 0.8307 (mmp) cc_final: 0.8025 (mmt) REVERT: C 48 MET cc_start: 0.8114 (ttm) cc_final: 0.7883 (ttt) REVERT: C 104 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7431 (mm-30) REVERT: C 170 LYS cc_start: 0.8166 (mttm) cc_final: 0.7887 (mttt) REVERT: C 216 LYS cc_start: 0.7717 (tttt) cc_final: 0.7457 (mtpt) REVERT: D 62 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7217 (mt-10) REVERT: D 98 SER cc_start: 0.9067 (p) cc_final: 0.8761 (p) REVERT: D 136 GLU cc_start: 0.7946 (tt0) cc_final: 0.7727 (tt0) REVERT: D 216 LYS cc_start: 0.8115 (tttt) cc_final: 0.7327 (mttp) REVERT: E 33 LEU cc_start: 0.8878 (tp) cc_final: 0.8590 (tt) REVERT: E 140 LYS cc_start: 0.8137 (ttmp) cc_final: 0.7819 (mtmt) REVERT: E 223 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6854 (mp0) REVERT: E 240 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7356 (ttmt) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.7460 time to fit residues: 240.4754 Evaluate side-chains 181 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS C 254 GLN D 134 GLN E 210 ASN E 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.139658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112402 restraints weight = 10825.890| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.48 r_work: 0.3061 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10372 Z= 0.126 Angle : 0.599 11.907 14014 Z= 0.310 Chirality : 0.041 0.123 1640 Planarity : 0.006 0.054 1763 Dihedral : 5.340 22.377 1371 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.31 % Allowed : 11.66 % Favored : 86.03 % 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: -3.78 (0.19), residues: 1312 helix: -2.53 (0.12), residues: 1096 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 89 TYR 0.020 0.002 TYR G 20 PHE 0.022 0.002 PHE A 121 TRP 0.006 0.001 TRP G 35 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00264 (10372) covalent geometry : angle 0.59941 (14014) hydrogen bonds : bond 0.04477 ( 644) hydrogen bonds : angle 4.97720 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.368 Fit side-chains REVERT: A 23 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7673 (pp20) REVERT: A 65 VAL cc_start: 0.8810 (t) cc_final: 0.8570 (p) REVERT: A 140 LYS cc_start: 0.8378 (ttmp) cc_final: 0.7964 (ttpp) REVERT: B 48 MET cc_start: 0.8448 (ttm) cc_final: 0.8146 (ttt) REVERT: B 62 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7676 (mt-10) REVERT: C 48 MET cc_start: 0.8784 (ttm) cc_final: 0.8497 (ttt) REVERT: C 68 LYS cc_start: 0.7917 (mppt) cc_final: 0.7659 (mtpp) REVERT: C 104 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7719 (mm-30) REVERT: C 112 MET cc_start: 0.8439 (mmm) cc_final: 0.8235 (mmm) REVERT: C 199 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8692 (mt) REVERT: D 138 HIS cc_start: 0.8124 (t70) cc_final: 0.7218 (t-170) REVERT: D 216 LYS cc_start: 0.8592 (tttt) cc_final: 0.7568 (mttp) REVERT: E 64 LYS cc_start: 0.7014 (mttm) cc_final: 0.6665 (ptpp) REVERT: E 68 LYS cc_start: 0.7247 (mptt) cc_final: 0.6901 (mptt) REVERT: E 123 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: E 140 LYS cc_start: 0.8380 (ttmp) cc_final: 0.8050 (mtmt) REVERT: E 223 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7628 (mp0) outliers start: 25 outliers final: 5 residues processed: 216 average time/residue: 0.6451 time to fit residues: 147.9970 Evaluate side-chains 178 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 122 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 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 138 HIS B 125 HIS E 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.109071 restraints weight = 10814.500| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.48 r_work: 0.3009 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10372 Z= 0.133 Angle : 0.570 14.442 14014 Z= 0.289 Chirality : 0.042 0.136 1640 Planarity : 0.004 0.037 1763 Dihedral : 5.010 21.548 1371 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.96 % Allowed : 14.80 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.76 (0.22), residues: 1312 helix: -1.22 (0.15), residues: 1071 sheet: None (None), residues: 0 loop : 0.23 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.016 0.002 TYR G 20 PHE 0.023 0.002 PHE C 149 TRP 0.005 0.001 TRP A 146 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00310 (10372) covalent geometry : angle 0.56974 (14014) hydrogen bonds : bond 0.03863 ( 644) hydrogen bonds : angle 4.33641 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.263 Fit side-chains REVERT: A 23 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: A 40 MET cc_start: 0.7433 (mpt) cc_final: 0.7166 (mpt) REVERT: A 140 LYS cc_start: 0.8398 (ttmp) cc_final: 0.7976 (ttpp) REVERT: B 48 MET cc_start: 0.8634 (ttm) cc_final: 0.8338 (ttt) REVERT: B 62 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7711 (mt-10) REVERT: B 137 GLU cc_start: 0.8119 (pt0) cc_final: 0.7906 (tp30) REVERT: C 48 MET cc_start: 0.8841 (ttm) cc_final: 0.8576 (ttt) REVERT: C 68 LYS cc_start: 0.7991 (mppt) cc_final: 0.7711 (mtpp) REVERT: C 104 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7772 (mm-30) REVERT: C 140 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7897 (ttmt) REVERT: D 216 LYS cc_start: 0.8618 (tttt) cc_final: 0.7610 (mttp) REVERT: D 252 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7432 (pt) REVERT: E 64 LYS cc_start: 0.6980 (mttm) cc_final: 0.6646 (ptpp) REVERT: E 140 LYS cc_start: 0.8409 (ttmp) cc_final: 0.8049 (mtmt) REVERT: E 223 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7499 (mp0) outliers start: 32 outliers final: 6 residues processed: 200 average time/residue: 0.6834 time to fit residues: 145.0282 Evaluate side-chains 175 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 138 HIS D 29 HIS E 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.108778 restraints weight = 10833.909| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.49 r_work: 0.2989 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10372 Z= 0.121 Angle : 0.543 11.752 14014 Z= 0.274 Chirality : 0.041 0.153 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.784 21.088 1371 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.50 % Allowed : 15.82 % Favored : 81.68 % 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: -0.97 (0.22), residues: 1312 helix: -0.58 (0.15), residues: 1091 sheet: None (None), residues: 0 loop : 0.03 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.014 0.002 TYR F 20 PHE 0.020 0.002 PHE A 121 TRP 0.006 0.001 TRP D 203 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00279 (10372) covalent geometry : angle 0.54294 (14014) hydrogen bonds : bond 0.03480 ( 644) hydrogen bonds : angle 4.05671 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.417 Fit side-chains REVERT: A 23 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7705 (pp20) REVERT: A 76 GLU cc_start: 0.7303 (tp30) cc_final: 0.7095 (tt0) REVERT: A 117 ASP cc_start: 0.7303 (m-30) cc_final: 0.7091 (m-30) REVERT: A 119 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6200 (mppt) REVERT: A 140 LYS cc_start: 0.8366 (ttmp) cc_final: 0.7934 (ttpp) REVERT: A 226 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7852 (tttm) REVERT: B 1 MET cc_start: 0.6269 (tmt) cc_final: 0.6019 (mpt) REVERT: B 48 MET cc_start: 0.8509 (ttm) cc_final: 0.8213 (ttt) REVERT: B 62 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7760 (mt-10) REVERT: B 137 GLU cc_start: 0.8087 (pt0) cc_final: 0.7873 (tp30) REVERT: C 48 MET cc_start: 0.8813 (ttm) cc_final: 0.8531 (ttt) REVERT: C 68 LYS cc_start: 0.7986 (mppt) cc_final: 0.7743 (mtpt) REVERT: C 104 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7751 (mm-30) REVERT: C 170 LYS cc_start: 0.7916 (mttm) cc_final: 0.7647 (mtpp) REVERT: D 216 LYS cc_start: 0.8611 (tttt) cc_final: 0.7603 (mttp) REVERT: D 252 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7387 (pt) REVERT: E 3 LEU cc_start: 0.7701 (mt) cc_final: 0.7470 (mm) REVERT: E 64 LYS cc_start: 0.6992 (mttm) cc_final: 0.6669 (ptpp) REVERT: E 99 ARG cc_start: 0.7256 (mtt90) cc_final: 0.6881 (mtp180) REVERT: E 140 LYS cc_start: 0.8410 (ttmp) cc_final: 0.8035 (mtmt) REVERT: E 223 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7534 (mp0) outliers start: 27 outliers final: 7 residues processed: 195 average time/residue: 0.7026 time to fit residues: 145.2125 Evaluate side-chains 179 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 35 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.104919 restraints weight = 10791.662| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.48 r_work: 0.2945 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10372 Z= 0.170 Angle : 0.588 14.926 14014 Z= 0.297 Chirality : 0.044 0.138 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.883 22.034 1371 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.13 % Allowed : 17.67 % Favored : 80.20 % 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: -0.52 (0.23), residues: 1312 helix: -0.31 (0.15), residues: 1081 sheet: None (None), residues: 0 loop : 0.43 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.016 0.002 TYR B 145 PHE 0.024 0.002 PHE C 149 TRP 0.007 0.002 TRP C 146 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00411 (10372) covalent geometry : angle 0.58781 (14014) hydrogen bonds : bond 0.03925 ( 644) hydrogen bonds : angle 4.13147 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.372 Fit side-chains REVERT: A 23 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7607 (pp20) REVERT: A 117 ASP cc_start: 0.7324 (m-30) cc_final: 0.7122 (m-30) REVERT: A 119 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6214 (mppt) REVERT: A 140 LYS cc_start: 0.8463 (ttmp) cc_final: 0.8030 (ttpp) REVERT: B 48 MET cc_start: 0.8561 (ttm) cc_final: 0.8257 (ttt) REVERT: C 48 MET cc_start: 0.8902 (ttm) cc_final: 0.8627 (ttt) REVERT: C 68 LYS cc_start: 0.8063 (mppt) cc_final: 0.7834 (mtpt) REVERT: C 104 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7735 (mm-30) REVERT: C 140 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7949 (ttmt) REVERT: C 170 LYS cc_start: 0.7955 (mttm) cc_final: 0.7652 (mtpp) REVERT: D 216 LYS cc_start: 0.8573 (tttt) cc_final: 0.7556 (mttp) REVERT: E 64 LYS cc_start: 0.7029 (mttm) cc_final: 0.6665 (ptpp) REVERT: E 99 ARG cc_start: 0.7347 (mtt90) cc_final: 0.6972 (mtp180) REVERT: E 140 LYS cc_start: 0.8435 (ttmp) cc_final: 0.8052 (mtmt) outliers start: 23 outliers final: 9 residues processed: 180 average time/residue: 0.7298 time to fit residues: 138.9375 Evaluate side-chains 173 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 80 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 95 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.107887 restraints weight = 10752.751| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.48 r_work: 0.3052 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10372 Z= 0.119 Angle : 0.535 12.511 14014 Z= 0.269 Chirality : 0.041 0.134 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.647 21.212 1371 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.04 % Allowed : 17.67 % Favored : 80.30 % 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: -0.07 (0.23), residues: 1312 helix: 0.03 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.38 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 251 TYR 0.012 0.002 TYR B 145 PHE 0.019 0.001 PHE A 121 TRP 0.007 0.001 TRP B 203 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00275 (10372) covalent geometry : angle 0.53493 (14014) hydrogen bonds : bond 0.03337 ( 644) hydrogen bonds : angle 3.90331 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.398 Fit side-chains REVERT: A 23 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7580 (pp20) REVERT: A 119 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6291 (mppt) REVERT: A 140 LYS cc_start: 0.8386 (ttmp) cc_final: 0.7960 (ttpp) REVERT: A 226 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8179 (ttpp) REVERT: B 48 MET cc_start: 0.8454 (ttm) cc_final: 0.8163 (ttt) REVERT: B 64 LYS cc_start: 0.8592 (ptmm) cc_final: 0.8060 (ptpt) REVERT: C 48 MET cc_start: 0.8825 (ttm) cc_final: 0.8529 (ttt) REVERT: C 68 LYS cc_start: 0.8141 (mppt) cc_final: 0.7924 (mtpt) REVERT: C 104 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7705 (mm-30) REVERT: C 140 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7904 (ttmt) REVERT: C 170 LYS cc_start: 0.7866 (mttm) cc_final: 0.7569 (mtpp) REVERT: D 216 LYS cc_start: 0.8561 (tttt) cc_final: 0.7572 (mttp) REVERT: E 3 LEU cc_start: 0.7716 (mt) cc_final: 0.7467 (mm) REVERT: E 64 LYS cc_start: 0.7117 (mttm) cc_final: 0.6748 (ptpp) REVERT: E 99 ARG cc_start: 0.7336 (mtt90) cc_final: 0.6931 (mtp180) REVERT: E 140 LYS cc_start: 0.8405 (ttmp) cc_final: 0.8038 (mtmt) outliers start: 22 outliers final: 5 residues processed: 180 average time/residue: 0.7240 time to fit residues: 138.0120 Evaluate side-chains 164 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 0.0060 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106048 restraints weight = 10692.807| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.47 r_work: 0.2996 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10372 Z= 0.145 Angle : 0.559 11.664 14014 Z= 0.281 Chirality : 0.042 0.138 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.688 21.671 1371 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.31 % Allowed : 18.32 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.14 (0.23), residues: 1312 helix: 0.17 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.48 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.014 0.002 TYR B 145 PHE 0.020 0.002 PHE C 121 TRP 0.006 0.001 TRP C 146 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00349 (10372) covalent geometry : angle 0.55902 (14014) hydrogen bonds : bond 0.03600 ( 644) hydrogen bonds : angle 3.95058 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.386 Fit side-chains REVERT: A 23 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7546 (pp20) REVERT: A 119 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6296 (mppt) REVERT: A 140 LYS cc_start: 0.8421 (ttmp) cc_final: 0.8004 (ttpp) REVERT: A 223 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7875 (tp30) REVERT: A 226 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8191 (ttpp) REVERT: B 48 MET cc_start: 0.8527 (ttm) cc_final: 0.8224 (ttt) REVERT: B 64 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8177 (ptmt) REVERT: B 137 GLU cc_start: 0.8303 (tp30) cc_final: 0.7885 (tt0) REVERT: B 140 LYS cc_start: 0.8616 (ttpt) cc_final: 0.7736 (mtmt) REVERT: C 48 MET cc_start: 0.8865 (ttm) cc_final: 0.8568 (ttt) REVERT: C 68 LYS cc_start: 0.8198 (mppt) cc_final: 0.7975 (mtpt) REVERT: C 104 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7694 (mm-30) REVERT: C 140 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7896 (ttmt) REVERT: C 170 LYS cc_start: 0.7881 (mttm) cc_final: 0.7567 (mtpp) REVERT: D 216 LYS cc_start: 0.8562 (tttt) cc_final: 0.7558 (mttp) REVERT: E 64 LYS cc_start: 0.7137 (mttm) cc_final: 0.6761 (ptpp) REVERT: E 99 ARG cc_start: 0.7340 (mtt90) cc_final: 0.6913 (mtp180) REVERT: E 140 LYS cc_start: 0.8418 (ttmp) cc_final: 0.8031 (mtmt) outliers start: 25 outliers final: 9 residues processed: 179 average time/residue: 0.7270 time to fit residues: 137.6456 Evaluate side-chains 177 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 0.0170 chunk 103 optimal weight: 3.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.136304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108134 restraints weight = 10661.689| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.44 r_work: 0.3015 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10372 Z= 0.118 Angle : 0.532 10.786 14014 Z= 0.268 Chirality : 0.041 0.136 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.557 21.165 1371 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.76 % Allowed : 18.87 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.23), residues: 1312 helix: 0.35 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.75 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 251 TYR 0.012 0.002 TYR C 197 PHE 0.019 0.001 PHE A 121 TRP 0.007 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00276 (10372) covalent geometry : angle 0.53219 (14014) hydrogen bonds : bond 0.03295 ( 644) hydrogen bonds : angle 3.83492 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.461 Fit side-chains REVERT: A 23 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7619 (pp20) REVERT: A 119 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6318 (mppt) REVERT: A 140 LYS cc_start: 0.8412 (ttmp) cc_final: 0.7968 (ttpp) REVERT: A 223 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: A 226 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8168 (ttpp) REVERT: B 1 MET cc_start: 0.6240 (tmt) cc_final: 0.6037 (mpt) REVERT: B 48 MET cc_start: 0.8460 (ttm) cc_final: 0.8155 (ttt) REVERT: B 64 LYS cc_start: 0.8606 (ptmm) cc_final: 0.8197 (ptmt) REVERT: B 137 GLU cc_start: 0.8229 (tp30) cc_final: 0.7879 (tt0) REVERT: B 140 LYS cc_start: 0.8589 (ttpt) cc_final: 0.7715 (mtmt) REVERT: C 48 MET cc_start: 0.8809 (ttm) cc_final: 0.8500 (ttt) REVERT: C 68 LYS cc_start: 0.8142 (mppt) cc_final: 0.7934 (mtpt) REVERT: C 104 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7694 (mm-30) REVERT: C 140 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7854 (ttmt) REVERT: C 170 LYS cc_start: 0.7788 (mttm) cc_final: 0.7498 (mtmt) REVERT: D 216 LYS cc_start: 0.8556 (tttt) cc_final: 0.7568 (mttp) REVERT: E 3 LEU cc_start: 0.7624 (mt) cc_final: 0.7380 (mm) REVERT: E 64 LYS cc_start: 0.7126 (mttm) cc_final: 0.6749 (ptpp) REVERT: E 99 ARG cc_start: 0.7290 (mtt90) cc_final: 0.6881 (mtp180) REVERT: E 140 LYS cc_start: 0.8420 (ttmp) cc_final: 0.8048 (mtmt) outliers start: 19 outliers final: 8 residues processed: 177 average time/residue: 0.7048 time to fit residues: 132.2077 Evaluate side-chains 172 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.106018 restraints weight = 10651.249| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.48 r_work: 0.3009 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10372 Z= 0.144 Angle : 0.562 13.658 14014 Z= 0.281 Chirality : 0.043 0.158 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.625 21.576 1371 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.76 % Allowed : 19.52 % Favored : 78.72 % 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: 0.47 (0.23), residues: 1312 helix: 0.37 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.77 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.015 0.002 TYR C 197 PHE 0.020 0.002 PHE C 121 TRP 0.006 0.001 TRP D 146 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00348 (10372) covalent geometry : angle 0.56231 (14014) hydrogen bonds : bond 0.03538 ( 644) hydrogen bonds : angle 3.91593 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.375 Fit side-chains REVERT: A 23 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7569 (pp20) REVERT: A 119 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6280 (mppt) REVERT: A 140 LYS cc_start: 0.8455 (ttmp) cc_final: 0.8015 (ttpp) REVERT: A 223 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: A 226 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8140 (ttpp) REVERT: B 48 MET cc_start: 0.8619 (ttm) cc_final: 0.8297 (ttt) REVERT: B 64 LYS cc_start: 0.8593 (ptmm) cc_final: 0.8181 (ptmt) REVERT: B 137 GLU cc_start: 0.8270 (tp30) cc_final: 0.7782 (tt0) REVERT: B 140 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8195 (mtpm) REVERT: C 48 MET cc_start: 0.8868 (ttm) cc_final: 0.8570 (ttt) REVERT: C 68 LYS cc_start: 0.8195 (mppt) cc_final: 0.7977 (mtpt) REVERT: C 104 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7704 (mm-30) REVERT: C 140 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7886 (ttmt) REVERT: C 170 LYS cc_start: 0.7830 (mttm) cc_final: 0.7540 (mtmt) REVERT: D 216 LYS cc_start: 0.8576 (tttt) cc_final: 0.7572 (mttp) REVERT: E 3 LEU cc_start: 0.7637 (mt) cc_final: 0.7390 (mm) REVERT: E 40 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7630 (mmt) REVERT: E 64 LYS cc_start: 0.7132 (mttm) cc_final: 0.6770 (ptpp) REVERT: E 99 ARG cc_start: 0.7299 (mtt90) cc_final: 0.6837 (mtp180) REVERT: E 140 LYS cc_start: 0.8413 (ttmp) cc_final: 0.8026 (mtmt) outliers start: 19 outliers final: 9 residues processed: 173 average time/residue: 0.6756 time to fit residues: 123.8384 Evaluate side-chains 176 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.105107 restraints weight = 10638.510| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.48 r_work: 0.2984 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10372 Z= 0.160 Angle : 0.581 13.391 14014 Z= 0.291 Chirality : 0.043 0.163 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.703 22.053 1371 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.57 % Allowed : 19.70 % Favored : 78.72 % 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: 0.45 (0.23), residues: 1312 helix: 0.36 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.79 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 251 TYR 0.016 0.002 TYR C 197 PHE 0.022 0.002 PHE C 121 TRP 0.006 0.001 TRP C 146 HIS 0.004 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00391 (10372) covalent geometry : angle 0.58105 (14014) hydrogen bonds : bond 0.03676 ( 644) hydrogen bonds : angle 3.97600 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.382 Fit side-chains REVERT: A 23 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7573 (pp20) REVERT: A 119 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6273 (mppt) REVERT: A 140 LYS cc_start: 0.8446 (ttmp) cc_final: 0.8001 (ttpp) REVERT: A 223 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7844 (tp30) REVERT: A 226 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8092 (ttpp) REVERT: B 48 MET cc_start: 0.8629 (ttm) cc_final: 0.8298 (ttt) REVERT: B 64 LYS cc_start: 0.8608 (ptmm) cc_final: 0.8181 (ptmt) REVERT: B 137 GLU cc_start: 0.8272 (tp30) cc_final: 0.7979 (tt0) REVERT: C 48 MET cc_start: 0.8866 (ttm) cc_final: 0.8571 (ttt) REVERT: C 68 LYS cc_start: 0.8195 (mppt) cc_final: 0.7968 (mtpt) REVERT: C 104 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7706 (mm-30) REVERT: C 140 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7926 (ttmt) REVERT: C 170 LYS cc_start: 0.7824 (mttm) cc_final: 0.7502 (mtpp) REVERT: D 216 LYS cc_start: 0.8559 (tttt) cc_final: 0.7537 (mttp) REVERT: E 40 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7592 (mmt) REVERT: E 64 LYS cc_start: 0.7147 (mttm) cc_final: 0.6787 (ptpp) REVERT: E 99 ARG cc_start: 0.7268 (mtt90) cc_final: 0.6776 (mtp180) REVERT: E 140 LYS cc_start: 0.8424 (ttmp) cc_final: 0.8034 (mtmt) REVERT: E 151 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7748 (tt0) outliers start: 17 outliers final: 9 residues processed: 175 average time/residue: 0.6893 time to fit residues: 127.6428 Evaluate side-chains 174 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 25 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.105515 restraints weight = 10711.630| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.48 r_work: 0.2973 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10372 Z= 0.150 Angle : 0.577 13.136 14014 Z= 0.288 Chirality : 0.043 0.146 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.672 21.762 1371 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.48 % Allowed : 19.61 % Favored : 78.91 % 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: 0.52 (0.23), residues: 1312 helix: 0.40 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.80 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 235 TYR 0.016 0.002 TYR C 197 PHE 0.021 0.002 PHE C 121 TRP 0.006 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00364 (10372) covalent geometry : angle 0.57745 (14014) hydrogen bonds : bond 0.03579 ( 644) hydrogen bonds : angle 3.94337 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.23 seconds wall clock time: 66 minutes 49.44 seconds (4009.44 seconds total)