Starting phenix.real_space_refine (version: dev) on Mon Dec 12 11:18:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/12_2022/6ykr_10830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/12_2022/6ykr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/12_2022/6ykr_10830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/12_2022/6ykr_10830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/12_2022/6ykr_10830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/12_2022/6ykr_10830.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 251": "NH1" <-> "NH2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 6.07, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 4.10 Conformation dependent library (CDL) restraints added in 1.6 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: 0.41 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: 2.75 Time building geometry restraints manager: 4.50 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: 99.15 - 106.12: 237 106.12 - 113.08: 5576 113.08 - 120.05: 4066 120.05 - 127.01: 4024 127.01 - 133.98: 111 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 2.440 nonbonded pdb=" OG SER D 246 " pdb=" OD1 ASP D 248 " model vdw 2.329 2.440 nonbonded pdb=" OG SER E 246 " pdb=" OD1 ASP E 248 " model vdw 2.345 2.440 nonbonded pdb=" OG SER A 246 " pdb=" OD1 ASP A 248 " model vdw 2.361 2.440 nonbonded pdb=" OD2 ASP B 20 " pdb=" O HOH B 301 " model vdw 2.378 2.440 ... (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 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 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. 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: 0.650 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: 0.020 Extract box with map and model: 4.350 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 29.480 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 1.4261 time to fit residues: 462.0928 Evaluate side-chains 173 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7017 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 254 GLN B 125 HIS C 254 GLN E 210 ASN E 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10372 Z= 0.255 Angle : 0.643 11.813 14014 Z= 0.332 Chirality : 0.043 0.133 1640 Planarity : 0.006 0.052 1763 Dihedral : 5.481 22.026 1371 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 3.15 % 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: -3.55 (0.19), residues: 1312 helix: -2.47 (0.12), residues: 1066 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 246 *********************** 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 fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 1.165 Fit side-chains outliers start: 34 outliers final: 7 residues processed: 219 average time/residue: 1.2800 time to fit residues: 299.7092 Evaluate side-chains 170 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1418 time to fit residues: 2.1296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10372 Z= 0.201 Angle : 0.570 14.830 14014 Z= 0.288 Chirality : 0.042 0.138 1640 Planarity : 0.004 0.038 1763 Dihedral : 5.067 21.641 1371 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.83 (0.22), residues: 1312 helix: -1.27 (0.15), residues: 1066 sheet: None (None), residues: 0 loop : 0.16 (0.41), residues: 246 *********************** 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 211 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.181 Fit side-chains outliers start: 35 outliers final: 9 residues processed: 198 average time/residue: 1.3562 time to fit residues: 286.1517 Evaluate side-chains 175 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.6289 time to fit residues: 3.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 124 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.8616 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10372 Z= 0.249 Angle : 0.583 12.184 14014 Z= 0.296 Chirality : 0.043 0.139 1640 Planarity : 0.004 0.036 1763 Dihedral : 5.002 21.872 1371 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1312 helix: -0.72 (0.15), residues: 1066 sheet: None (None), residues: 0 loop : 0.36 (0.42), residues: 246 *********************** 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 197 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.223 Fit side-chains outliers start: 27 outliers final: 10 residues processed: 188 average time/residue: 1.3530 time to fit residues: 271.2496 Evaluate side-chains 171 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.8149 time to fit residues: 3.5223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 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 80 GLN A 138 HIS E 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4006 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= 0.148 Angle : 0.527 14.672 14014 Z= 0.264 Chirality : 0.040 0.201 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.675 20.813 1371 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.23), residues: 1312 helix: -0.27 (0.15), residues: 1091 sheet: None (None), residues: 0 loop : 0.19 (0.42), residues: 221 *********************** 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 196 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 1.134 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 190 average time/residue: 1.2864 time to fit residues: 261.4517 Evaluate side-chains 165 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.7065 time to fit residues: 3.3202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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: 0.8564 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10372 Z= 0.164 Angle : 0.529 12.270 14014 Z= 0.265 Chirality : 0.041 0.166 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.604 20.829 1371 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 1.94 % 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: -0.09 (0.23), residues: 1312 helix: 0.04 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.30 (0.42), residues: 221 *********************** 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 183 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.257 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 175 average time/residue: 1.3968 time to fit residues: 260.5699 Evaluate side-chains 159 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.6293 time to fit residues: 3.3655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 77 optimal weight: 0.0470 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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: 0.8551 moved from start: 0.4204 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= 0.156 Angle : 0.521 11.176 14014 Z= 0.260 Chirality : 0.040 0.133 1640 Planarity : 0.003 0.034 1763 Dihedral : 4.506 20.576 1371 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1312 helix: 0.25 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.62 (0.44), residues: 211 *********************** 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 184 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.202 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 179 average time/residue: 1.3469 time to fit residues: 257.6430 Evaluate side-chains 163 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.1119 time to fit residues: 2.7850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8557 moved from start: 0.4265 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= 0.167 Angle : 0.532 13.173 14014 Z= 0.264 Chirality : 0.041 0.136 1640 Planarity : 0.003 0.033 1763 Dihedral : 4.505 20.742 1371 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 1.57 % 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: 0.48 (0.23), residues: 1312 helix: 0.39 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.72 (0.45), residues: 211 *********************** 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 178 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 1.205 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 174 average time/residue: 1.3965 time to fit residues: 258.8582 Evaluate side-chains 161 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.6567 time to fit residues: 3.4017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 90 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8573 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10372 Z= 0.192 Angle : 0.547 12.541 14014 Z= 0.272 Chirality : 0.041 0.136 1640 Planarity : 0.003 0.033 1763 Dihedral : 4.544 21.017 1371 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.85 % 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: 0.57 (0.23), residues: 1312 helix: 0.45 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.71 (0.44), residues: 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.246 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 171 average time/residue: 1.3662 time to fit residues: 249.2729 Evaluate side-chains 162 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.9660 time to fit residues: 4.7849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 0.0000 chunk 128 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 overall best weight: 0.5362 ------------------------------------------------------------------------------- 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: 0.8536 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10372 Z= 0.148 Angle : 0.527 12.821 14014 Z= 0.260 Chirality : 0.040 0.130 1640 Planarity : 0.003 0.033 1763 Dihedral : 4.416 20.294 1371 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.93 % 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: 1.02 (0.23), residues: 1312 helix: 0.77 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : 0.80 (0.42), residues: 241 ********************** 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 164 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 1.293 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 161 average time/residue: 1.3154 time to fit residues: 226.4283 Evaluate side-chains 155 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2446 time to fit residues: 2.0556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 42 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.135765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107261 restraints weight = 10516.037| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.45 r_work: 0.2967 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10372 Z= 0.188 Angle : 0.550 12.595 14014 Z= 0.272 Chirality : 0.041 0.137 1640 Planarity : 0.003 0.033 1763 Dihedral : 4.495 20.930 1371 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.02 % 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: 1.04 (0.23), residues: 1312 helix: 0.80 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : 0.75 (0.42), residues: 241 =============================================================================== Job complete usr+sys time: 4406.26 seconds wall clock time: 78 minutes 35.05 seconds (4715.05 seconds total)