Starting phenix.real_space_refine on Mon Jul 28 02:53:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ykr_10830/07_2025/6ykr_10830.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ykr_10830/07_2025/6ykr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ykr_10830/07_2025/6ykr_10830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ykr_10830/07_2025/6ykr_10830.map" model { file = "/net/cci-nas-00/data/ceres_data/6ykr_10830/07_2025/6ykr_10830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ykr_10830/07_2025/6ykr_10830.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.58, per 1000 atoms: 0.65 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.03 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: 3.18 Time building geometry restraints manager: 3.00 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.670 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.270 ------------------------------------------------------------------------------- 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 : 2.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP B 203 HIS 0.006 0.001 HIS B 52 PHE 0.055 0.003 PHE C 149 TYR 0.012 0.003 TYR A 197 ARG 0.002 0.000 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.30038 ( 644) hydrogen bonds : angle 11.62447 ( 1893) covalent geometry : bond 0.00448 (10372) covalent geometry : angle 0.83946 (14014) *********************** 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 : 1.155 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: 0.7432 (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: 0.8136 (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: 1.5487 time to fit residues: 500.6253 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 : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 C 254 GLN D 134 GLN E 210 ASN E 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109599 restraints weight = 10786.710| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.47 r_work: 0.3014 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10372 Z= 0.153 Angle : 0.624 11.896 14014 Z= 0.322 Chirality : 0.042 0.131 1640 Planarity : 0.006 0.053 1763 Dihedral : 5.443 22.245 1371 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.68 % Allowed : 11.56 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.19), residues: 1312 helix: -2.53 (0.12), residues: 1096 sheet: None (None), residues: 0 loop : -0.68 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 146 HIS 0.004 0.001 HIS B 52 PHE 0.027 0.002 PHE C 149 TYR 0.020 0.003 TYR G 20 ARG 0.002 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 644) hydrogen bonds : angle 5.00591 ( 1893) covalent geometry : bond 0.00352 (10372) covalent geometry : angle 0.62383 (14014) *********************** 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 231 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 1.191 Fit side-chains REVERT: A 23 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7634 (pp20) REVERT: A 37 LEU cc_start: 0.7968 (mt) cc_final: 0.7699 (mm) REVERT: A 65 VAL cc_start: 0.8875 (t) cc_final: 0.8657 (p) REVERT: A 140 LYS cc_start: 0.8378 (ttmp) cc_final: 0.7961 (ttpp) REVERT: B 48 MET cc_start: 0.8572 (ttm) cc_final: 0.8253 (ttt) REVERT: B 62 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7706 (mt-10) REVERT: B 136 GLU cc_start: 0.8346 (tt0) cc_final: 0.8133 (tt0) REVERT: C 48 MET cc_start: 0.8822 (ttm) cc_final: 0.8550 (ttt) REVERT: C 68 LYS cc_start: 0.7980 (mppt) cc_final: 0.7717 (mtpp) REVERT: C 91 ASP cc_start: 0.7866 (m-30) cc_final: 0.7650 (m-30) REVERT: C 104 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7712 (mm-30) REVERT: C 112 MET cc_start: 0.8468 (mmm) cc_final: 0.8251 (mmm) REVERT: D 216 LYS cc_start: 0.8593 (tttt) cc_final: 0.7567 (mttp) REVERT: E 64 LYS cc_start: 0.7008 (mttm) cc_final: 0.6656 (ptpp) REVERT: E 140 LYS cc_start: 0.8418 (ttmp) cc_final: 0.8078 (mtmt) outliers start: 29 outliers final: 6 residues processed: 221 average time/residue: 1.4766 time to fit residues: 347.5988 Evaluate side-chains 182 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 175 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 E residue 42 THR Chi-restraints excluded: chain E residue 94 LEU 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 39 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.106734 restraints weight = 10890.553| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.48 r_work: 0.2970 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10372 Z= 0.157 Angle : 0.592 15.026 14014 Z= 0.300 Chirality : 0.043 0.136 1640 Planarity : 0.005 0.038 1763 Dihedral : 5.133 21.888 1371 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.24 % Allowed : 14.62 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1312 helix: -1.29 (0.14), residues: 1071 sheet: None (None), residues: 0 loop : 0.27 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 146 HIS 0.004 0.001 HIS B 125 PHE 0.025 0.002 PHE C 149 TYR 0.015 0.002 TYR B 145 ARG 0.002 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 644) hydrogen bonds : angle 4.41548 ( 1893) covalent geometry : bond 0.00376 (10372) covalent geometry : angle 0.59162 (14014) *********************** 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 214 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.158 Fit side-chains REVERT: A 23 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: A 119 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6278 (mppt) REVERT: A 122 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: A 140 LYS cc_start: 0.8396 (ttmp) cc_final: 0.7954 (ttpp) REVERT: B 48 MET cc_start: 0.8636 (ttm) cc_final: 0.8309 (ttt) REVERT: B 62 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7826 (mt-10) REVERT: B 137 GLU cc_start: 0.8114 (pt0) cc_final: 0.7909 (tp30) REVERT: C 48 MET cc_start: 0.8892 (ttm) cc_final: 0.8615 (ttt) REVERT: C 68 LYS cc_start: 0.8072 (mppt) cc_final: 0.7830 (mtpt) REVERT: C 91 ASP cc_start: 0.7931 (m-30) cc_final: 0.7664 (m-30) REVERT: C 104 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7736 (mm-30) REVERT: C 140 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7934 (ttmt) REVERT: D 216 LYS cc_start: 0.8601 (tttt) cc_final: 0.7569 (mttp) REVERT: E 64 LYS cc_start: 0.7040 (mttm) cc_final: 0.6667 (ptpp) REVERT: E 140 LYS cc_start: 0.8439 (ttmp) cc_final: 0.8078 (mtmt) outliers start: 35 outliers final: 7 residues processed: 201 average time/residue: 1.4620 time to fit residues: 312.3859 Evaluate side-chains 180 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 137 GLU 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 51 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.136224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.108480 restraints weight = 10698.916| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.47 r_work: 0.3037 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3737 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 : 0.541 12.058 14014 Z= 0.273 Chirality : 0.041 0.135 1640 Planarity : 0.004 0.036 1763 Dihedral : 4.810 21.156 1371 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.31 % Allowed : 15.91 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1312 helix: -0.59 (0.15), residues: 1081 sheet: None (None), residues: 0 loop : 0.34 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.002 PHE A 121 TYR 0.013 0.002 TYR F 20 ARG 0.002 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 644) hydrogen bonds : angle 4.05354 ( 1893) covalent geometry : bond 0.00272 (10372) covalent geometry : angle 0.54069 (14014) *********************** 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 205 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.286 Fit side-chains REVERT: A 23 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7699 (pp20) REVERT: A 119 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6321 (mppt) REVERT: A 140 LYS cc_start: 0.8392 (ttmp) cc_final: 0.7945 (ttpp) REVERT: B 48 MET cc_start: 0.8556 (ttm) cc_final: 0.8265 (ttt) REVERT: B 62 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7871 (mt-10) REVERT: C 48 MET cc_start: 0.8833 (ttm) cc_final: 0.8546 (ttt) REVERT: C 91 ASP cc_start: 0.7918 (m-30) cc_final: 0.7660 (m-30) REVERT: C 104 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7750 (mm-30) REVERT: D 216 LYS cc_start: 0.8583 (tttt) cc_final: 0.7587 (mttp) REVERT: E 3 LEU cc_start: 0.7752 (mt) cc_final: 0.7525 (mm) REVERT: E 64 LYS cc_start: 0.7016 (mttm) cc_final: 0.6681 (ptpp) REVERT: E 99 ARG cc_start: 0.7308 (mtt90) cc_final: 0.6901 (mtp180) REVERT: E 140 LYS cc_start: 0.8407 (ttmp) cc_final: 0.8030 (mtmt) outliers start: 25 outliers final: 7 residues processed: 197 average time/residue: 1.4437 time to fit residues: 302.6774 Evaluate side-chains 172 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS 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 122 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 109 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.134496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.106859 restraints weight = 10728.855| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.45 r_work: 0.2980 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10372 Z= 0.133 Angle : 0.549 14.673 14014 Z= 0.275 Chirality : 0.042 0.166 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.742 21.399 1371 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.31 % Allowed : 16.93 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1312 helix: -0.20 (0.15), residues: 1081 sheet: None (None), residues: 0 loop : 0.47 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 146 HIS 0.003 0.001 HIS B 52 PHE 0.020 0.002 PHE A 121 TYR 0.013 0.002 TYR B 145 ARG 0.001 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 644) hydrogen bonds : angle 3.98178 ( 1893) covalent geometry : bond 0.00312 (10372) covalent geometry : angle 0.54944 (14014) *********************** 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 188 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.795 Fit side-chains REVERT: A 23 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7649 (pp20) REVERT: A 37 LEU cc_start: 0.7885 (mm) cc_final: 0.7678 (mt) REVERT: A 119 LYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6262 (mppt) REVERT: A 140 LYS cc_start: 0.8424 (ttmp) cc_final: 0.7979 (ttpp) REVERT: A 226 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8192 (ttpp) REVERT: B 48 MET cc_start: 0.8550 (ttm) cc_final: 0.8238 (ttt) REVERT: B 140 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8330 (mtpm) REVERT: C 48 MET cc_start: 0.8839 (ttm) cc_final: 0.8543 (ttt) REVERT: C 91 ASP cc_start: 0.7905 (m-30) cc_final: 0.7639 (m-30) REVERT: C 104 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7688 (mm-30) REVERT: C 140 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7689 (ttmt) REVERT: D 216 LYS cc_start: 0.8554 (tttt) cc_final: 0.7546 (mttp) REVERT: D 252 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7374 (pt) REVERT: E 3 LEU cc_start: 0.7694 (mt) cc_final: 0.7465 (mm) REVERT: E 64 LYS cc_start: 0.7006 (mttm) cc_final: 0.6624 (ptpp) REVERT: E 99 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6933 (mtp180) REVERT: E 140 LYS cc_start: 0.8421 (ttmp) cc_final: 0.8029 (mtmt) outliers start: 25 outliers final: 11 residues processed: 177 average time/residue: 2.0370 time to fit residues: 381.6555 Evaluate side-chains 173 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 48 MET Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 212 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104249 restraints weight = 10832.413| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.46 r_work: 0.2961 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10372 Z= 0.172 Angle : 0.583 13.014 14014 Z= 0.294 Chirality : 0.043 0.142 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.845 21.961 1371 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.96 % Allowed : 16.65 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1312 helix: -0.08 (0.15), residues: 1081 sheet: None (None), residues: 0 loop : 0.53 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 146 HIS 0.004 0.001 HIS B 52 PHE 0.023 0.002 PHE C 149 TYR 0.016 0.002 TYR B 145 ARG 0.002 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 644) hydrogen bonds : angle 4.06171 ( 1893) covalent geometry : bond 0.00419 (10372) covalent geometry : angle 0.58319 (14014) *********************** 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 197 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.273 Fit side-chains REVERT: A 23 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7569 (pp20) REVERT: A 37 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7697 (mt) REVERT: A 119 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6321 (mppt) REVERT: A 140 LYS cc_start: 0.8450 (ttmp) cc_final: 0.8007 (ttpp) REVERT: B 48 MET cc_start: 0.8604 (ttm) cc_final: 0.8282 (ttt) REVERT: B 137 GLU cc_start: 0.8255 (tp30) cc_final: 0.7977 (tt0) REVERT: C 48 MET cc_start: 0.8901 (ttm) cc_final: 0.8612 (ttt) REVERT: C 91 ASP cc_start: 0.7903 (m-30) cc_final: 0.7618 (m-30) REVERT: C 104 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7704 (mm-30) REVERT: C 140 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7903 (ttmt) REVERT: C 170 LYS cc_start: 0.7940 (mttm) cc_final: 0.7569 (mtpp) REVERT: D 216 LYS cc_start: 0.8551 (tttt) cc_final: 0.7517 (mttp) REVERT: E 64 LYS cc_start: 0.7065 (mttm) cc_final: 0.6670 (ptpp) REVERT: E 99 ARG cc_start: 0.7353 (mtt90) cc_final: 0.6925 (mtp180) REVERT: E 140 LYS cc_start: 0.8435 (ttmp) cc_final: 0.8052 (mtmt) outliers start: 32 outliers final: 11 residues processed: 183 average time/residue: 1.9616 time to fit residues: 382.2680 Evaluate side-chains 172 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 37 LEU 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 122 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 98 SER 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 E residue 97 GLU 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 7 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.133757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105910 restraints weight = 10902.036| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.46 r_work: 0.2973 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10372 Z= 0.132 Angle : 0.550 11.698 14014 Z= 0.276 Chirality : 0.042 0.139 1640 Planarity : 0.004 0.036 1763 Dihedral : 4.691 21.360 1371 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.59 % Allowed : 17.48 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1312 helix: 0.12 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.44 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 203 HIS 0.003 0.001 HIS B 52 PHE 0.020 0.002 PHE A 121 TYR 0.013 0.002 TYR B 145 ARG 0.001 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 644) hydrogen bonds : angle 3.92812 ( 1893) covalent geometry : bond 0.00312 (10372) covalent geometry : angle 0.55018 (14014) *********************** 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 191 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.271 Fit side-chains REVERT: A 23 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7522 (pp20) REVERT: A 37 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7679 (mt) REVERT: A 119 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6259 (mppt) REVERT: A 140 LYS cc_start: 0.8438 (ttmp) cc_final: 0.8000 (ttpp) REVERT: B 48 MET cc_start: 0.8604 (ttm) cc_final: 0.8283 (ttt) REVERT: B 137 GLU cc_start: 0.8114 (tp30) cc_final: 0.7695 (tt0) REVERT: B 140 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8087 (mtpm) REVERT: C 48 MET cc_start: 0.8858 (ttm) cc_final: 0.8546 (ttt) REVERT: C 91 ASP cc_start: 0.7904 (m-30) cc_final: 0.7613 (m-30) REVERT: C 104 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7712 (mm-30) REVERT: C 140 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7831 (ttmt) REVERT: C 170 LYS cc_start: 0.7893 (mttm) cc_final: 0.7548 (mtmt) REVERT: D 178 MET cc_start: 0.7382 (ttm) cc_final: 0.7165 (tpt) REVERT: D 216 LYS cc_start: 0.8550 (tttt) cc_final: 0.7526 (mttp) REVERT: E 64 LYS cc_start: 0.7132 (mttm) cc_final: 0.6713 (ptpp) REVERT: E 99 ARG cc_start: 0.7374 (mtt90) cc_final: 0.6930 (mtp180) REVERT: E 140 LYS cc_start: 0.8410 (ttmp) cc_final: 0.8029 (mtmt) outliers start: 28 outliers final: 10 residues processed: 179 average time/residue: 1.5391 time to fit residues: 292.4028 Evaluate side-chains 171 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 37 LEU 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 B residue 140 LYS 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 98 SER 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 121 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.0060 chunk 69 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.135744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107938 restraints weight = 10760.017| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.45 r_work: 0.3003 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10372 Z= 0.111 Angle : 0.528 10.855 14014 Z= 0.264 Chirality : 0.041 0.179 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.528 20.847 1371 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.94 % Allowed : 18.32 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1312 helix: 0.35 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.76 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 203 HIS 0.004 0.000 HIS B 52 PHE 0.018 0.001 PHE A 121 TYR 0.012 0.002 TYR G 20 ARG 0.001 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 644) hydrogen bonds : angle 3.81775 ( 1893) covalent geometry : bond 0.00255 (10372) covalent geometry : angle 0.52770 (14014) *********************** 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 190 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 1.194 Fit side-chains REVERT: A 23 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7512 (pp20) REVERT: A 37 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7725 (mt) REVERT: A 57 LYS cc_start: 0.8821 (tttt) cc_final: 0.8311 (tttp) REVERT: A 119 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6174 (mppt) REVERT: A 140 LYS cc_start: 0.8439 (ttmp) cc_final: 0.8007 (ttpp) REVERT: A 226 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8199 (ttpp) REVERT: B 1 MET cc_start: 0.6278 (tmt) cc_final: 0.6058 (mpt) REVERT: B 48 MET cc_start: 0.8625 (ttm) cc_final: 0.8294 (ttt) REVERT: B 137 GLU cc_start: 0.8090 (tp30) cc_final: 0.7698 (tt0) REVERT: B 140 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8102 (mtpm) REVERT: C 48 MET cc_start: 0.8841 (ttm) cc_final: 0.8494 (ttt) REVERT: C 91 ASP cc_start: 0.7916 (m-30) cc_final: 0.7638 (m-30) REVERT: C 104 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7718 (mm-30) REVERT: C 140 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7771 (ttmt) REVERT: C 170 LYS cc_start: 0.7889 (mttm) cc_final: 0.7559 (mtmt) REVERT: D 129 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8169 (mt-10) REVERT: D 216 LYS cc_start: 0.8546 (tttt) cc_final: 0.7537 (mttp) REVERT: D 252 ILE cc_start: 0.7608 (mp) cc_final: 0.7282 (pt) REVERT: E 3 LEU cc_start: 0.7646 (mt) cc_final: 0.7405 (mm) REVERT: E 64 LYS cc_start: 0.7147 (mttm) cc_final: 0.6749 (ptpp) REVERT: E 99 ARG cc_start: 0.7339 (mtt90) cc_final: 0.6883 (mtp180) REVERT: E 140 LYS cc_start: 0.8411 (ttmp) cc_final: 0.8047 (mtmt) outliers start: 21 outliers final: 5 residues processed: 180 average time/residue: 1.4268 time to fit residues: 273.3233 Evaluate side-chains 173 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 140 LYS 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 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 86 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 = 0.134671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.106128 restraints weight = 10673.188| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.48 r_work: 0.3002 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10372 Z= 0.134 Angle : 0.560 13.671 14014 Z= 0.278 Chirality : 0.042 0.159 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.580 21.188 1371 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.85 % Allowed : 19.70 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1312 helix: 0.41 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.76 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 146 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.002 PHE C 121 TYR 0.016 0.002 TYR C 197 ARG 0.001 0.000 ARG C 251 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 644) hydrogen bonds : angle 3.87618 ( 1893) covalent geometry : bond 0.00321 (10372) covalent geometry : angle 0.55958 (14014) *********************** 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 179 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.184 Fit side-chains REVERT: A 23 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7515 (pp20) REVERT: A 119 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6272 (mppt) REVERT: A 140 LYS cc_start: 0.8446 (ttmp) cc_final: 0.8025 (ttpp) REVERT: A 223 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7905 (tp30) REVERT: A 226 LYS cc_start: 0.8490 (ttpt) cc_final: 0.8188 (ttpp) REVERT: B 48 MET cc_start: 0.8638 (ttm) cc_final: 0.8293 (ttt) REVERT: B 137 GLU cc_start: 0.8165 (tp30) cc_final: 0.7745 (tt0) REVERT: B 140 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8144 (mtpm) REVERT: C 48 MET cc_start: 0.8848 (ttm) cc_final: 0.8548 (ttt) REVERT: C 91 ASP cc_start: 0.7912 (m-30) cc_final: 0.7640 (m-30) REVERT: C 104 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7702 (mm-30) REVERT: C 140 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7834 (ttmt) REVERT: C 170 LYS cc_start: 0.7903 (mttm) cc_final: 0.7577 (mtmt) REVERT: D 216 LYS cc_start: 0.8580 (tttt) cc_final: 0.7569 (mttp) REVERT: E 16 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6304 (mm) REVERT: E 64 LYS cc_start: 0.7133 (mttm) cc_final: 0.6739 (ptpp) REVERT: E 99 ARG cc_start: 0.7318 (mtt90) cc_final: 0.6838 (mtp180) REVERT: E 140 LYS cc_start: 0.8400 (ttmp) cc_final: 0.8015 (mtmt) outliers start: 20 outliers final: 5 residues processed: 170 average time/residue: 1.4755 time to fit residues: 266.6250 Evaluate side-chains 168 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 140 LYS 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 E residue 16 ILE 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 66 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.108152 restraints weight = 10709.667| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.43 r_work: 0.2995 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10372 Z= 0.116 Angle : 0.543 13.099 14014 Z= 0.269 Chirality : 0.041 0.153 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.496 20.827 1371 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.48 % Allowed : 20.35 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1312 helix: 0.55 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.82 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 203 HIS 0.004 0.001 HIS B 52 PHE 0.018 0.001 PHE A 121 TYR 0.015 0.002 TYR C 197 ARG 0.001 0.000 ARG D 235 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 644) hydrogen bonds : angle 3.80821 ( 1893) covalent geometry : bond 0.00271 (10372) covalent geometry : angle 0.54343 (14014) ********************** 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 177 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 1.217 Fit side-chains REVERT: A 23 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: A 119 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6183 (mppt) REVERT: A 140 LYS cc_start: 0.8424 (ttmp) cc_final: 0.7986 (ttpp) REVERT: A 223 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: A 226 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8148 (ttpp) REVERT: B 48 MET cc_start: 0.8598 (ttm) cc_final: 0.8244 (ttt) REVERT: B 137 GLU cc_start: 0.8136 (tp30) cc_final: 0.7742 (tt0) REVERT: B 140 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8118 (mtpm) REVERT: C 48 MET cc_start: 0.8789 (ttm) cc_final: 0.8483 (ttt) REVERT: C 91 ASP cc_start: 0.7875 (m-30) cc_final: 0.7604 (m-30) REVERT: C 104 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7681 (mm-30) REVERT: C 140 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7780 (ttmt) REVERT: C 170 LYS cc_start: 0.7872 (mttm) cc_final: 0.7540 (mtmt) REVERT: D 216 LYS cc_start: 0.8564 (tttt) cc_final: 0.7560 (mttp) REVERT: D 252 ILE cc_start: 0.7591 (mp) cc_final: 0.7259 (pt) REVERT: E 16 ILE cc_start: 0.6442 (OUTLIER) cc_final: 0.6165 (mm) REVERT: E 64 LYS cc_start: 0.7106 (mttm) cc_final: 0.6687 (ptpp) REVERT: E 99 ARG cc_start: 0.7202 (mtt90) cc_final: 0.6751 (mtp180) REVERT: E 140 LYS cc_start: 0.8398 (ttmp) cc_final: 0.8021 (mtmt) outliers start: 16 outliers final: 6 residues processed: 170 average time/residue: 1.4809 time to fit residues: 267.5977 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 : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 37 LEU 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 140 LYS Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain E residue 16 ILE 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 97 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 35 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.137067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109093 restraints weight = 10697.783| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.43 r_work: 0.3015 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10372 Z= 0.111 Angle : 0.536 12.623 14014 Z= 0.265 Chirality : 0.041 0.147 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.425 20.436 1371 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.30 % Allowed : 20.63 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1312 helix: 0.85 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : 0.90 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 203 HIS 0.003 0.000 HIS B 52 PHE 0.017 0.001 PHE A 121 TYR 0.014 0.002 TYR C 197 ARG 0.001 0.000 ARG D 235 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 644) hydrogen bonds : angle 3.74531 ( 1893) covalent geometry : bond 0.00256 (10372) covalent geometry : angle 0.53591 (14014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9518.53 seconds wall clock time: 168 minutes 37.77 seconds (10117.77 seconds total)