Starting phenix.real_space_refine on Sun Dec 29 05:53:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ykr_10830/12_2024/6ykr_10830.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ykr_10830/12_2024/6ykr_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_10830/12_2024/6ykr_10830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ykr_10830/12_2024/6ykr_10830.map" model { file = "/net/cci-nas-00/data/ceres_data/6ykr_10830/12_2024/6ykr_10830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ykr_10830/12_2024/6ykr_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-5532/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: 6.40, per 1000 atoms: 0.63 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: 2.56 Conformation dependent library (CDL) restraints added in 1.4 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: 0.78 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: 2.73 Time building geometry restraints manager: 2.94 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.760 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- 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 : 1.220 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: 1.6315 time to fit residues: 527.3665 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 : 1.104 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.884 Fit side-chains REVERT: A 23 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7378 (pp20) REVERT: A 37 LEU cc_start: 0.8127 (mt) cc_final: 0.7924 (mm) REVERT: A 140 LYS cc_start: 0.7873 (ttmp) cc_final: 0.7608 (ttpp) REVERT: B 48 MET cc_start: 0.8057 (ttm) cc_final: 0.7793 (ttt) REVERT: B 62 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7387 (mt-10) REVERT: B 136 GLU cc_start: 0.7598 (tt0) cc_final: 0.7353 (tt0) REVERT: C 48 MET cc_start: 0.8324 (ttm) cc_final: 0.8107 (ttt) REVERT: C 104 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7448 (mm-30) REVERT: C 112 MET cc_start: 0.7911 (mmm) cc_final: 0.7698 (mmm) REVERT: D 216 LYS cc_start: 0.8066 (tttt) cc_final: 0.7255 (mttp) REVERT: E 112 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7696 (mmm) REVERT: E 140 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7599 (mtmt) outliers start: 29 outliers final: 6 residues processed: 221 average time/residue: 1.4295 time to fit residues: 336.1922 Evaluate side-chains 180 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 E residue 112 MET 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 65 optimal weight: 0.0870 chunk 36 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 E 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10372 Z= 0.163 Angle : 0.552 14.496 14014 Z= 0.278 Chirality : 0.041 0.131 1640 Planarity : 0.004 0.037 1763 Dihedral : 4.948 21.320 1371 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.68 % Allowed : 15.17 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.22), residues: 1312 helix: -1.21 (0.15), residues: 1071 sheet: None (None), residues: 0 loop : 0.26 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 203 HIS 0.003 0.001 HIS B 125 PHE 0.021 0.002 PHE A 121 TYR 0.016 0.002 TYR G 20 ARG 0.002 0.000 ARG A 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 206 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.088 Fit side-chains REVERT: A 23 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: A 37 LEU cc_start: 0.8140 (mt) cc_final: 0.7925 (mm) REVERT: A 119 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6259 (mppt) REVERT: A 140 LYS cc_start: 0.7864 (ttmp) cc_final: 0.7549 (ttpp) REVERT: B 48 MET cc_start: 0.8003 (ttm) cc_final: 0.7746 (ttt) REVERT: B 62 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7432 (mt-10) REVERT: B 136 GLU cc_start: 0.7591 (tt0) cc_final: 0.7382 (tt0) REVERT: C 48 MET cc_start: 0.8286 (ttm) cc_final: 0.8051 (ttt) REVERT: C 129 GLU cc_start: 0.6927 (pt0) cc_final: 0.6604 (pp20) REVERT: D 216 LYS cc_start: 0.8052 (tttt) cc_final: 0.7278 (mttp) REVERT: E 3 LEU cc_start: 0.8229 (mt) cc_final: 0.7950 (mm) REVERT: E 15 SER cc_start: 0.8267 (m) cc_final: 0.7856 (t) REVERT: E 140 LYS cc_start: 0.7922 (ttmp) cc_final: 0.7569 (mtmt) REVERT: E 223 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6602 (mp0) outliers start: 29 outliers final: 5 residues processed: 194 average time/residue: 1.4508 time to fit residues: 299.6838 Evaluate side-chains 173 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 D residue 137 GLU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 223 GLU 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 115 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 124 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3749 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= 0.201 Angle : 0.556 12.180 14014 Z= 0.280 Chirality : 0.042 0.136 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.847 21.559 1371 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.59 % Allowed : 16.37 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1312 helix: -0.58 (0.15), residues: 1081 sheet: None (None), residues: 0 loop : 0.28 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 146 HIS 0.004 0.001 HIS A 138 PHE 0.021 0.002 PHE A 121 TYR 0.014 0.002 TYR B 145 ARG 0.001 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 207 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 1.068 Fit side-chains REVERT: A 23 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: A 119 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6211 (mppt) REVERT: A 140 LYS cc_start: 0.7884 (ttmp) cc_final: 0.7550 (ttpp) REVERT: A 226 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7948 (ttpp) REVERT: B 48 MET cc_start: 0.8016 (ttm) cc_final: 0.7775 (ttt) REVERT: B 62 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7435 (mt-10) REVERT: B 136 GLU cc_start: 0.7618 (tt0) cc_final: 0.7413 (tt0) REVERT: C 48 MET cc_start: 0.8305 (ttm) cc_final: 0.8071 (ttt) REVERT: C 140 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7397 (ttmt) REVERT: D 216 LYS cc_start: 0.8058 (tttt) cc_final: 0.7270 (mttp) REVERT: D 252 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7548 (pt) REVERT: E 3 LEU cc_start: 0.8157 (mt) cc_final: 0.7896 (mm) REVERT: E 140 LYS cc_start: 0.7942 (ttmp) cc_final: 0.7556 (mtmt) outliers start: 28 outliers final: 10 residues processed: 195 average time/residue: 1.4961 time to fit residues: 309.6300 Evaluate side-chains 181 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 7.9990 chunk 70 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.0170 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10372 Z= 0.175 Angle : 0.539 14.509 14014 Z= 0.270 Chirality : 0.041 0.134 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.673 21.160 1371 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.68 % Allowed : 16.28 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.23), residues: 1312 helix: -0.17 (0.15), residues: 1091 sheet: None (None), residues: 0 loop : 0.24 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 203 HIS 0.004 0.001 HIS B 52 PHE 0.020 0.001 PHE A 121 TYR 0.012 0.002 TYR B 145 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 201 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.087 Fit side-chains REVERT: A 23 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: A 119 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6233 (mppt) REVERT: A 140 LYS cc_start: 0.7892 (ttmp) cc_final: 0.7568 (ttpp) REVERT: A 226 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7957 (ttpp) REVERT: B 48 MET cc_start: 0.7915 (ttm) cc_final: 0.7698 (ttt) REVERT: B 62 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7523 (mt-10) REVERT: B 140 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7847 (mtpm) REVERT: C 48 MET cc_start: 0.8275 (ttm) cc_final: 0.8036 (ttt) REVERT: C 140 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7381 (ttmt) REVERT: D 216 LYS cc_start: 0.8016 (tttt) cc_final: 0.7256 (mttp) REVERT: D 252 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7515 (pt) REVERT: E 3 LEU cc_start: 0.8094 (mt) cc_final: 0.7815 (mm) REVERT: E 140 LYS cc_start: 0.7943 (ttmp) cc_final: 0.7557 (mtmt) outliers start: 29 outliers final: 10 residues processed: 187 average time/residue: 1.5220 time to fit residues: 303.0152 Evaluate side-chains 176 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 64 LYS 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 41 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 0.0060 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS D 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10372 Z= 0.157 Angle : 0.523 12.275 14014 Z= 0.262 Chirality : 0.041 0.130 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.550 20.737 1371 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 17.67 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1312 helix: 0.13 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.61 (0.44), residues: 211 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 B 145 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 197 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.233 Fit side-chains REVERT: A 23 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: A 37 LEU cc_start: 0.8115 (mm) cc_final: 0.7793 (mt) REVERT: A 119 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6231 (mppt) REVERT: A 140 LYS cc_start: 0.7872 (ttmp) cc_final: 0.7543 (ttpp) REVERT: A 226 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7868 (ttpp) REVERT: B 48 MET cc_start: 0.7860 (ttm) cc_final: 0.7646 (ttt) REVERT: B 62 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7501 (mt-10) REVERT: B 140 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7560 (mtmt) REVERT: C 48 MET cc_start: 0.8275 (ttm) cc_final: 0.7993 (ttt) REVERT: C 140 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7371 (ttmt) REVERT: D 129 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7548 (mt-10) REVERT: D 216 LYS cc_start: 0.8005 (tttt) cc_final: 0.7261 (mttp) REVERT: D 252 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7497 (pt) REVERT: E 3 LEU cc_start: 0.7987 (mt) cc_final: 0.7715 (mm) REVERT: E 15 SER cc_start: 0.8331 (m) cc_final: 0.7895 (t) REVERT: E 140 LYS cc_start: 0.7944 (ttmp) cc_final: 0.7568 (mtmt) outliers start: 29 outliers final: 8 residues processed: 185 average time/residue: 1.4887 time to fit residues: 292.9889 Evaluate side-chains 171 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 48 MET Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 64 LYS 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 14 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10372 Z= 0.150 Angle : 0.524 11.185 14014 Z= 0.261 Chirality : 0.041 0.158 1640 Planarity : 0.003 0.033 1763 Dihedral : 4.469 20.458 1371 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.85 % Allowed : 18.13 % Favored : 80.02 % 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: 0.46 (0.23), residues: 1312 helix: 0.37 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.77 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 203 HIS 0.003 0.000 HIS B 52 PHE 0.017 0.001 PHE A 121 TYR 0.012 0.002 TYR C 197 ARG 0.001 0.000 ARG D 235 *********************** 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 188 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.172 Fit side-chains REVERT: A 23 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7269 (pp20) REVERT: A 37 LEU cc_start: 0.8140 (mm) cc_final: 0.7810 (mt) REVERT: A 140 LYS cc_start: 0.7871 (ttmp) cc_final: 0.7575 (ttpp) REVERT: A 226 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7711 (tttm) REVERT: B 48 MET cc_start: 0.7846 (ttm) cc_final: 0.7638 (ttt) REVERT: B 62 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7519 (mt-10) REVERT: B 140 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7571 (mtmt) REVERT: C 48 MET cc_start: 0.8272 (ttm) cc_final: 0.8008 (ttt) REVERT: C 140 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7353 (ttmt) REVERT: D 129 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7540 (mt-10) REVERT: D 216 LYS cc_start: 0.7989 (tttt) cc_final: 0.7255 (mttp) REVERT: D 252 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7466 (pt) REVERT: E 15 SER cc_start: 0.8293 (m) cc_final: 0.7875 (t) REVERT: E 140 LYS cc_start: 0.7946 (ttmp) cc_final: 0.7582 (mtmt) outliers start: 20 outliers final: 6 residues processed: 178 average time/residue: 1.5310 time to fit residues: 289.6526 Evaluate side-chains 171 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 155 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 49 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.0070 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4149 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= 0.190 Angle : 0.554 13.404 14014 Z= 0.274 Chirality : 0.042 0.148 1640 Planarity : 0.004 0.033 1763 Dihedral : 4.539 21.020 1371 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.85 % Allowed : 19.15 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.54 (0.23), residues: 1312 helix: 0.43 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.75 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 146 HIS 0.004 0.001 HIS B 52 PHE 0.019 0.002 PHE A 121 TYR 0.015 0.002 TYR C 197 ARG 0.001 0.000 ARG D 99 *********************** 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 185 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.984 Fit side-chains REVERT: A 23 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7222 (pp20) REVERT: A 37 LEU cc_start: 0.8150 (mm) cc_final: 0.7908 (mt) REVERT: A 140 LYS cc_start: 0.7893 (ttmp) cc_final: 0.7576 (ttpp) REVERT: A 223 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: A 226 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7973 (ttpp) REVERT: B 48 MET cc_start: 0.7946 (ttm) cc_final: 0.7684 (ttt) REVERT: B 64 LYS cc_start: 0.8357 (ptmm) cc_final: 0.7972 (ptpt) REVERT: B 140 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7584 (mtmt) REVERT: C 48 MET cc_start: 0.8289 (ttm) cc_final: 0.8034 (ttt) REVERT: C 140 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7385 (ttmt) REVERT: D 216 LYS cc_start: 0.8013 (tttt) cc_final: 0.7239 (mttp) REVERT: E 3 LEU cc_start: 0.7998 (mt) cc_final: 0.7732 (mm) REVERT: E 140 LYS cc_start: 0.7950 (ttmp) cc_final: 0.7572 (mtmt) outliers start: 20 outliers final: 11 residues processed: 175 average time/residue: 1.5147 time to fit residues: 281.4774 Evaluate side-chains 175 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4179 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= 0.190 Angle : 0.553 12.630 14014 Z= 0.274 Chirality : 0.042 0.134 1640 Planarity : 0.004 0.033 1763 Dihedral : 4.525 21.055 1371 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.57 % Allowed : 19.98 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1312 helix: 0.51 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.78 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.002 PHE A 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 177 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.177 Fit side-chains REVERT: A 23 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: A 37 LEU cc_start: 0.8158 (mm) cc_final: 0.7911 (mt) REVERT: A 140 LYS cc_start: 0.7927 (ttmp) cc_final: 0.7583 (ttpp) REVERT: A 223 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7124 (tp30) REVERT: A 226 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7978 (ttpp) REVERT: B 48 MET cc_start: 0.8014 (ttm) cc_final: 0.7737 (ttt) REVERT: B 64 LYS cc_start: 0.8375 (ptmm) cc_final: 0.8097 (ptmt) REVERT: B 140 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7584 (mtmt) REVERT: C 48 MET cc_start: 0.8287 (ttm) cc_final: 0.8014 (ttt) REVERT: C 140 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7377 (ttmt) REVERT: D 216 LYS cc_start: 0.8014 (tttt) cc_final: 0.7259 (mttp) REVERT: D 252 ILE cc_start: 0.7732 (mp) cc_final: 0.7442 (pt) REVERT: E 3 LEU cc_start: 0.8022 (mt) cc_final: 0.7749 (mm) REVERT: E 140 LYS cc_start: 0.7929 (ttmp) cc_final: 0.7548 (mtmt) outliers start: 17 outliers final: 9 residues processed: 170 average time/residue: 1.6089 time to fit residues: 290.3544 Evaluate side-chains 170 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 127 SER 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 42 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10372 Z= 0.152 Angle : 0.535 12.169 14014 Z= 0.264 Chirality : 0.041 0.132 1640 Planarity : 0.003 0.033 1763 Dihedral : 4.416 20.488 1371 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.39 % Allowed : 20.17 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1312 helix: 0.66 (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 175 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.217 Fit side-chains REVERT: A 23 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: A 37 LEU cc_start: 0.8161 (mm) cc_final: 0.7915 (mt) REVERT: A 140 LYS cc_start: 0.7903 (ttmp) cc_final: 0.7564 (ttpp) REVERT: A 226 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7980 (ttpp) REVERT: B 48 MET cc_start: 0.7917 (ttm) cc_final: 0.7654 (ttt) REVERT: B 64 LYS cc_start: 0.8385 (ptmm) cc_final: 0.8110 (ptmt) REVERT: B 140 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7530 (mtmt) REVERT: C 48 MET cc_start: 0.8276 (ttm) cc_final: 0.7955 (ttt) REVERT: C 140 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7370 (ttmt) REVERT: D 129 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7596 (mt-10) REVERT: D 216 LYS cc_start: 0.7998 (tttt) cc_final: 0.7254 (mttp) REVERT: D 252 ILE cc_start: 0.7696 (mp) cc_final: 0.7394 (pt) REVERT: E 1 MET cc_start: 0.5925 (ttm) cc_final: 0.5587 (ttt) REVERT: E 3 LEU cc_start: 0.7889 (mt) cc_final: 0.7605 (mm) REVERT: E 140 LYS cc_start: 0.7956 (ttmp) cc_final: 0.7587 (mtmt) outliers start: 15 outliers final: 8 residues processed: 169 average time/residue: 1.5301 time to fit residues: 275.4532 Evaluate side-chains 166 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain F residue 18 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.0040 chunk 42 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.138033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110023 restraints weight = 10535.961| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.42 r_work: 0.3064 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10372 Z= 0.155 Angle : 0.535 11.790 14014 Z= 0.264 Chirality : 0.041 0.132 1640 Planarity : 0.003 0.033 1763 Dihedral : 4.386 20.411 1371 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.30 % Allowed : 20.54 % 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: 1.02 (0.23), residues: 1312 helix: 0.76 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.92 (0.45), residues: 211 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 0.017 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: 4756.08 seconds wall clock time: 85 minutes 40.83 seconds (5140.83 seconds total)