Starting phenix.real_space_refine on Fri Feb 14 07:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ykr_10830/02_2025/6ykr_10830.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ykr_10830/02_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_10830/02_2025/6ykr_10830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ykr_10830/02_2025/6ykr_10830.map" model { file = "/net/cci-nas-00/data/ceres_data/6ykr_10830/02_2025/6ykr_10830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ykr_10830/02_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-5592/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: 6.24, per 1000 atoms: 0.61 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: 2.55 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: 0.98 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: 2.96 Time building geometry restraints manager: 2.93 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: 1.240 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.780 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- 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= 0.283 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 *********************** 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 : 1.225 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: 1.5963 time to fit residues: 516.0037 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 : 1.147 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109598 restraints weight = 10786.711| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.47 r_work: 0.3011 rms_B_bonded: 2.36 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: 0.8439 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= 0.219 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 *********************** 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 : 1.064 Fit side-chains REVERT: A 23 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7634 (pp20) REVERT: A 37 LEU cc_start: 0.7973 (mt) cc_final: 0.7705 (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: 0.8252 (ttt) REVERT: B 62 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7706 (mt-10) REVERT: B 136 GLU cc_start: 0.8346 (tt0) cc_final: 0.8134 (tt0) REVERT: C 48 MET cc_start: 0.8822 (ttm) cc_final: 0.8550 (ttt) REVERT: C 68 LYS cc_start: 0.7981 (mppt) cc_final: 0.7718 (mtpp) REVERT: C 91 ASP cc_start: 0.7865 (m-30) cc_final: 0.7650 (m-30) REVERT: C 104 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7714 (mm-30) REVERT: C 112 MET cc_start: 0.8468 (mmm) cc_final: 0.8250 (mmm) REVERT: D 216 LYS cc_start: 0.8592 (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: 0.8417 (ttmp) cc_final: 0.8077 (mtmt) outliers start: 29 outliers final: 6 residues processed: 221 average time/residue: 1.4601 time to fit residues: 343.6306 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 : 1.189 ------------------------------------------------------------------------------- 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: 4.9990 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 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: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.133480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105366 restraints weight = 10915.327| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.48 r_work: 0.2954 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10372 Z= 0.275 Angle : 0.616 15.454 14014 Z= 0.312 Chirality : 0.044 0.141 1640 Planarity : 0.005 0.038 1763 Dihedral : 5.223 22.157 1371 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.24 % Allowed : 14.71 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.22), residues: 1312 helix: -1.33 (0.14), residues: 1071 sheet: None (None), residues: 0 loop : 0.26 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 146 HIS 0.005 0.001 HIS B 125 PHE 0.028 0.002 PHE C 149 TYR 0.017 0.003 TYR B 145 ARG 0.002 0.000 ARG C 251 *********************** 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 213 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.160 Fit side-chains REVERT: A 23 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7663 (pp20) REVERT: A 57 LYS cc_start: 0.8852 (tttt) cc_final: 0.8328 (tttm) REVERT: A 119 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6276 (mppt) REVERT: A 122 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: A 140 LYS cc_start: 0.8408 (ttmp) cc_final: 0.7960 (ttpp) REVERT: B 48 MET cc_start: 0.8604 (ttm) cc_final: 0.8270 (ttt) REVERT: B 62 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7871 (mt-10) REVERT: B 137 GLU cc_start: 0.8113 (pt0) cc_final: 0.7889 (tp30) REVERT: B 178 MET cc_start: 0.7550 (ppp) cc_final: 0.7329 (ptp) REVERT: C 48 MET cc_start: 0.8904 (ttm) cc_final: 0.8623 (ttt) REVERT: C 68 LYS cc_start: 0.8069 (mppt) cc_final: 0.7826 (mtpt) REVERT: C 91 ASP cc_start: 0.7977 (m-30) cc_final: 0.7722 (m-30) REVERT: C 104 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7707 (mm-30) REVERT: C 140 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7950 (ttmt) REVERT: D 216 LYS cc_start: 0.8582 (tttt) cc_final: 0.7543 (mttp) REVERT: E 64 LYS cc_start: 0.7011 (mttm) cc_final: 0.6642 (ptpp) REVERT: E 140 LYS cc_start: 0.8422 (ttmp) cc_final: 0.8054 (mtmt) outliers start: 35 outliers final: 9 residues processed: 200 average time/residue: 1.4912 time to fit residues: 316.9217 Evaluate side-chains 184 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 68 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.135745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107919 restraints weight = 10692.696| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.47 r_work: 0.3000 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3704 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= 0.171 Angle : 0.540 12.212 14014 Z= 0.274 Chirality : 0.041 0.139 1640 Planarity : 0.004 0.037 1763 Dihedral : 4.842 21.294 1371 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -0.96 (0.23), residues: 1312 helix: -0.62 (0.15), residues: 1081 sheet: None (None), residues: 0 loop : 0.29 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 PHE 0.020 0.002 PHE A 121 TYR 0.014 0.002 TYR F 20 ARG 0.002 0.000 ARG C 251 *********************** 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 202 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.171 Fit side-chains REVERT: A 23 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7701 (pp20) REVERT: A 119 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6340 (mppt) REVERT: A 140 LYS cc_start: 0.8384 (ttmp) cc_final: 0.7916 (ttpp) REVERT: B 48 MET cc_start: 0.8583 (ttm) cc_final: 0.8281 (ttt) REVERT: B 62 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7803 (mt-10) REVERT: C 48 MET cc_start: 0.8840 (ttm) cc_final: 0.8557 (ttt) REVERT: C 68 LYS cc_start: 0.8069 (mppt) cc_final: 0.7865 (mtpt) REVERT: C 91 ASP cc_start: 0.7970 (m-30) cc_final: 0.7715 (m-30) REVERT: C 104 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7732 (mm-30) REVERT: D 216 LYS cc_start: 0.8579 (tttt) cc_final: 0.7574 (mttp) REVERT: E 3 LEU cc_start: 0.7801 (mt) cc_final: 0.7577 (mm) REVERT: E 64 LYS cc_start: 0.7005 (mttm) cc_final: 0.6666 (ptpp) REVERT: E 99 ARG cc_start: 0.7322 (mtt90) cc_final: 0.6932 (mtp180) REVERT: E 140 LYS cc_start: 0.8413 (ttmp) cc_final: 0.8041 (mtmt) outliers start: 25 outliers final: 8 residues processed: 193 average time/residue: 1.4655 time to fit residues: 300.9798 Evaluate side-chains 174 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 C residue 122 GLU 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: 0.8980 chunk 117 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 109 optimal weight: 0.0370 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.135682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108216 restraints weight = 10701.557| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.43 r_work: 0.2993 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10372 Z= 0.161 Angle : 0.538 14.658 14014 Z= 0.268 Chirality : 0.041 0.144 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.657 21.026 1371 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.41 % Allowed : 16.65 % Favored : 80.94 % 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: -0.37 (0.23), residues: 1312 helix: -0.17 (0.15), residues: 1091 sheet: None (None), residues: 0 loop : 0.25 (0.42), residues: 221 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 0.001 PHE A 121 TYR 0.012 0.002 TYR F 20 ARG 0.001 0.000 ARG C 251 *********************** 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 194 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.057 Fit side-chains REVERT: A 23 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7628 (pp20) REVERT: A 37 LEU cc_start: 0.7884 (mm) cc_final: 0.7675 (mt) REVERT: A 65 VAL cc_start: 0.8740 (t) cc_final: 0.8405 (p) REVERT: A 119 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6315 (mppt) REVERT: A 140 LYS cc_start: 0.8371 (ttmp) cc_final: 0.7939 (ttpp) REVERT: A 226 LYS cc_start: 0.8417 (ttpt) cc_final: 0.7819 (tttm) REVERT: B 1 MET cc_start: 0.6284 (tmt) cc_final: 0.6060 (mpt) REVERT: B 48 MET cc_start: 0.8556 (ttm) cc_final: 0.8244 (ttt) REVERT: B 62 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7866 (mt-10) REVERT: B 140 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8276 (mtpm) REVERT: C 48 MET cc_start: 0.8806 (ttm) cc_final: 0.8506 (ttt) REVERT: C 68 LYS cc_start: 0.8036 (mppt) cc_final: 0.7827 (mtpt) REVERT: C 91 ASP cc_start: 0.7951 (m-30) cc_final: 0.7692 (m-30) REVERT: C 104 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7679 (mm-30) REVERT: C 140 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7781 (ttmt) REVERT: D 216 LYS cc_start: 0.8556 (tttt) cc_final: 0.7546 (mttp) REVERT: D 252 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7366 (pt) REVERT: E 3 LEU cc_start: 0.7634 (mt) cc_final: 0.7402 (mm) REVERT: E 64 LYS cc_start: 0.7075 (mttm) cc_final: 0.6649 (ptpp) REVERT: E 99 ARG cc_start: 0.7314 (mtt90) cc_final: 0.6931 (mtp180) REVERT: E 140 LYS cc_start: 0.8441 (ttmp) cc_final: 0.8064 (mtmt) outliers start: 26 outliers final: 8 residues processed: 184 average time/residue: 1.4956 time to fit residues: 292.6310 Evaluate side-chains 174 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 16 ILE 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: 0.0870 chunk 76 optimal weight: 4.9990 chunk 81 optimal weight: 0.0000 chunk 83 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.5762 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.137002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109616 restraints weight = 10704.212| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.42 r_work: 0.3013 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10372 Z= 0.152 Angle : 0.521 12.314 14014 Z= 0.260 Chirality : 0.040 0.142 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.523 20.615 1371 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.04 % Allowed : 17.39 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1312 helix: 0.17 (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 D 203 HIS 0.003 0.000 HIS B 52 PHE 0.018 0.001 PHE A 121 TYR 0.011 0.002 TYR C 197 ARG 0.001 0.000 ARG D 235 *********************** 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 195 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 1.198 Fit side-chains REVERT: A 23 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7587 (pp20) REVERT: A 37 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7538 (mt) REVERT: A 65 VAL cc_start: 0.8772 (t) cc_final: 0.8483 (p) REVERT: A 119 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6325 (mppt) REVERT: A 140 LYS cc_start: 0.8400 (ttmp) cc_final: 0.7970 (ttpp) REVERT: A 226 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8131 (ttpp) REVERT: B 1 MET cc_start: 0.6269 (tmt) cc_final: 0.5990 (mpt) REVERT: B 48 MET cc_start: 0.8529 (ttm) cc_final: 0.8218 (ttt) REVERT: B 140 LYS cc_start: 0.8496 (ttpt) cc_final: 0.7782 (mtmt) REVERT: C 48 MET cc_start: 0.8804 (ttm) cc_final: 0.8492 (ttt) REVERT: C 68 LYS cc_start: 0.8044 (mppt) cc_final: 0.7836 (mtpt) REVERT: C 104 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7643 (mm-30) REVERT: C 140 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7734 (ttmt) REVERT: C 170 LYS cc_start: 0.7911 (mttm) cc_final: 0.7595 (mtmt) REVERT: D 216 LYS cc_start: 0.8531 (tttt) cc_final: 0.7536 (mttp) REVERT: D 252 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7359 (pt) REVERT: E 3 LEU cc_start: 0.7541 (mt) cc_final: 0.7299 (mm) REVERT: E 15 SER cc_start: 0.8085 (m) cc_final: 0.7565 (t) REVERT: E 64 LYS cc_start: 0.7086 (mttm) cc_final: 0.6687 (ptpp) REVERT: E 99 ARG cc_start: 0.7323 (mtt90) cc_final: 0.6941 (mtp180) REVERT: E 140 LYS cc_start: 0.8438 (ttmp) cc_final: 0.8069 (mtmt) outliers start: 22 outliers final: 6 residues processed: 187 average time/residue: 1.4527 time to fit residues: 288.6797 Evaluate side-chains 173 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 65 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104538 restraints weight = 10919.748| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.47 r_work: 0.2944 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10372 Z= 0.258 Angle : 0.579 11.770 14014 Z= 0.290 Chirality : 0.043 0.143 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.726 21.862 1371 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.50 % Allowed : 17.58 % 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: 0.11 (0.23), residues: 1312 helix: 0.15 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.48 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 146 HIS 0.004 0.001 HIS B 52 PHE 0.023 0.002 PHE C 149 TYR 0.015 0.002 TYR B 145 ARG 0.002 0.000 ARG C 251 *********************** 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 197 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 1.186 Fit side-chains REVERT: A 23 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: A 119 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6289 (mppt) REVERT: A 140 LYS cc_start: 0.8463 (ttmp) cc_final: 0.8039 (ttpp) REVERT: B 48 MET cc_start: 0.8676 (ttm) cc_final: 0.8339 (ttt) REVERT: B 140 LYS cc_start: 0.8579 (ttpt) cc_final: 0.7791 (mtmt) REVERT: C 48 MET cc_start: 0.8859 (ttm) cc_final: 0.8558 (ttt) REVERT: C 68 LYS cc_start: 0.8242 (mppt) cc_final: 0.7986 (mtpt) REVERT: C 91 ASP cc_start: 0.7899 (m-30) cc_final: 0.7611 (m-30) REVERT: C 104 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7705 (mm-30) REVERT: C 140 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7879 (ttmt) REVERT: C 170 LYS cc_start: 0.7917 (mttm) cc_final: 0.7583 (mtmt) REVERT: D 178 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7190 (tpt) REVERT: D 216 LYS cc_start: 0.8552 (tttt) cc_final: 0.7531 (mttp) REVERT: E 64 LYS cc_start: 0.7143 (mttm) cc_final: 0.6733 (ptpp) REVERT: E 99 ARG cc_start: 0.7347 (mtt90) cc_final: 0.6956 (mtp180) REVERT: E 140 LYS cc_start: 0.8433 (ttmp) cc_final: 0.8056 (mtmt) outliers start: 27 outliers final: 6 residues processed: 185 average time/residue: 1.4681 time to fit residues: 288.8267 Evaluate side-chains 177 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 178 MET 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: 0.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.135362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.107447 restraints weight = 10783.779| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.45 r_work: 0.2994 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10372 Z= 0.176 Angle : 0.540 10.744 14014 Z= 0.270 Chirality : 0.041 0.161 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.572 21.103 1371 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.48 % Allowed : 19.15 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.23), residues: 1312 helix: 0.36 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.75 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 203 HIS 0.003 0.001 HIS B 52 PHE 0.018 0.001 PHE A 121 TYR 0.013 0.002 TYR C 197 ARG 0.001 0.000 ARG D 235 *********************** 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 183 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 1.101 Fit side-chains REVERT: A 23 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7498 (pp20) REVERT: A 119 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6280 (mppt) REVERT: A 140 LYS cc_start: 0.8431 (ttmp) cc_final: 0.7992 (ttpp) REVERT: A 226 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8235 (ttpp) REVERT: B 48 MET cc_start: 0.8554 (ttm) cc_final: 0.8232 (ttt) REVERT: B 140 LYS cc_start: 0.8514 (ttpt) cc_final: 0.7755 (mtmt) REVERT: C 48 MET cc_start: 0.8837 (ttm) cc_final: 0.8531 (ttt) REVERT: C 91 ASP cc_start: 0.7895 (m-30) cc_final: 0.7617 (m-30) REVERT: C 104 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7691 (mm-30) REVERT: C 140 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7803 (ttmt) REVERT: C 170 LYS cc_start: 0.7875 (mttm) cc_final: 0.7541 (mtmt) REVERT: D 216 LYS cc_start: 0.8555 (tttt) cc_final: 0.7537 (mttp) REVERT: D 252 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7273 (pt) REVERT: E 3 LEU cc_start: 0.7638 (mt) cc_final: 0.7399 (mm) REVERT: E 16 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6319 (mm) REVERT: E 64 LYS cc_start: 0.7157 (mttm) cc_final: 0.6758 (ptpp) REVERT: E 99 ARG cc_start: 0.7302 (mtt90) cc_final: 0.6866 (mtp180) REVERT: E 140 LYS cc_start: 0.8385 (ttmp) cc_final: 0.8038 (mtmt) outliers start: 16 outliers final: 5 residues processed: 178 average time/residue: 1.4414 time to fit residues: 273.1081 Evaluate side-chains 174 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 16 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 86 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.105890 restraints weight = 10694.206| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.47 r_work: 0.2973 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10372 Z= 0.209 Angle : 0.566 13.620 14014 Z= 0.280 Chirality : 0.042 0.147 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.614 21.457 1371 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.04 % Allowed : 19.80 % 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: 0.51 (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 C 146 HIS 0.004 0.001 HIS B 52 PHE 0.020 0.002 PHE C 121 TYR 0.015 0.002 TYR C 197 ARG 0.001 0.000 ARG C 251 *********************** 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 182 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.096 Fit side-chains REVERT: A 23 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7499 (pp20) REVERT: A 119 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6287 (mppt) REVERT: A 140 LYS cc_start: 0.8447 (ttmp) cc_final: 0.8012 (ttpp) REVERT: A 223 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: A 226 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8139 (ttpp) REVERT: B 48 MET cc_start: 0.8628 (ttm) cc_final: 0.8281 (ttt) REVERT: B 140 LYS cc_start: 0.8567 (ttpt) cc_final: 0.7765 (mtmt) REVERT: C 48 MET cc_start: 0.8860 (ttm) cc_final: 0.8560 (ttt) REVERT: C 91 ASP cc_start: 0.7901 (m-30) cc_final: 0.7615 (m-30) REVERT: C 104 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7695 (mm-30) REVERT: C 140 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7842 (ttmt) REVERT: C 170 LYS cc_start: 0.7895 (mttm) cc_final: 0.7571 (mtmt) REVERT: D 216 LYS cc_start: 0.8562 (tttt) cc_final: 0.7541 (mttp) REVERT: E 16 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6399 (mm) REVERT: E 64 LYS cc_start: 0.7134 (mttm) cc_final: 0.6752 (ptpp) REVERT: E 99 ARG cc_start: 0.7299 (mtt90) cc_final: 0.6830 (mtp180) REVERT: E 140 LYS cc_start: 0.8400 (ttmp) cc_final: 0.8030 (mtmt) outliers start: 22 outliers final: 8 residues processed: 172 average time/residue: 1.5025 time to fit residues: 274.6582 Evaluate side-chains 170 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain E residue 16 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 124 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.137169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.109137 restraints weight = 10684.903| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.43 r_work: 0.3020 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10372 Z= 0.157 Angle : 0.536 12.727 14014 Z= 0.265 Chirality : 0.041 0.138 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.465 20.712 1371 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.02 % Allowed : 20.44 % Favored : 78.54 % 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: 0.78 (0.23), residues: 1312 helix: 0.59 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.85 (0.45), residues: 211 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 0.013 0.002 TYR C 197 ARG 0.001 0.000 ARG D 235 ********************** 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 174 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.129 Fit side-chains REVERT: A 23 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7494 (pp20) REVERT: A 140 LYS cc_start: 0.8385 (ttmp) cc_final: 0.7945 (ttpp) REVERT: A 226 LYS cc_start: 0.8421 (ttpt) cc_final: 0.8108 (ttpp) REVERT: B 1 MET cc_start: 0.6172 (tmt) cc_final: 0.5918 (mpt) REVERT: B 48 MET cc_start: 0.8578 (ttm) cc_final: 0.8231 (ttt) REVERT: B 140 LYS cc_start: 0.8485 (ttpt) cc_final: 0.7689 (mtmt) REVERT: C 48 MET cc_start: 0.8778 (ttm) cc_final: 0.8426 (ttt) REVERT: C 104 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7662 (mm-30) REVERT: C 140 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7734 (ttmt) REVERT: C 170 LYS cc_start: 0.7867 (mttm) cc_final: 0.7530 (mtmt) REVERT: D 129 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8139 (mt-10) REVERT: D 216 LYS cc_start: 0.8540 (tttt) cc_final: 0.7518 (mttp) REVERT: D 252 ILE cc_start: 0.7554 (mp) cc_final: 0.7255 (pt) REVERT: E 16 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.6187 (mm) REVERT: E 64 LYS cc_start: 0.7072 (mttm) cc_final: 0.6675 (ptpp) REVERT: E 99 ARG cc_start: 0.7190 (mtt90) cc_final: 0.6757 (mtp180) REVERT: E 140 LYS cc_start: 0.8367 (ttmp) cc_final: 0.8018 (mtmt) outliers start: 11 outliers final: 6 residues processed: 170 average time/residue: 1.5047 time to fit residues: 271.9524 Evaluate side-chains 168 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 16 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 97 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 35 optimal weight: 0.0270 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.137559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109458 restraints weight = 10671.414| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.43 r_work: 0.2995 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4285 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= 0.156 Angle : 0.538 12.365 14014 Z= 0.265 Chirality : 0.041 0.133 1640 Planarity : 0.003 0.035 1763 Dihedral : 4.419 20.650 1371 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.30 % Allowed : 20.81 % Favored : 77.89 % 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: 1.18 (0.23), residues: 1312 helix: 0.90 (0.16), residues: 1066 sheet: None (None), residues: 0 loop : 0.79 (0.42), residues: 246 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7786.55 seconds wall clock time: 138 minutes 5.30 seconds (8285.30 seconds total)