Starting phenix.real_space_refine on Fri Mar 15 00:30:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/03_2024/6ykr_10830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/03_2024/6ykr_10830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/03_2024/6ykr_10830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/03_2024/6ykr_10830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ykr_10830/03_2024/6ykr_10830.pdb" } 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 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-5265/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: 5.43, per 1000 atoms: 0.53 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 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: 0.89 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: 2.58 Time building geometry restraints manager: 3.96 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 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: 2.450 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: 4.040 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 27.790 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.180 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.299 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: 1.4992 time to fit residues: 484.7853 Evaluate side-chains 181 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 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 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: 0.8160 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10372 Z= 0.208 Angle : 0.619 11.956 14014 Z= 0.319 Chirality : 0.042 0.132 1640 Planarity : 0.006 0.053 1763 Dihedral : 5.417 22.137 1371 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.59 % Allowed : 11.75 % Favored : 85.66 % 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: -3.85 (0.19), residues: 1312 helix: -2.58 (0.12), residues: 1096 sheet: None (None), residues: 0 loop : -0.73 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 146 HIS 0.003 0.001 HIS B 52 PHE 0.025 0.002 PHE C 149 TYR 0.019 0.002 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 227 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.228 Fit side-chains REVERT: A 23 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7373 (pp20) REVERT: A 140 LYS cc_start: 0.7895 (ttmp) cc_final: 0.7630 (ttpp) REVERT: B 48 MET cc_start: 0.8066 (ttm) cc_final: 0.7794 (ttt) REVERT: B 62 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7379 (mt-10) REVERT: B 136 GLU cc_start: 0.7616 (tt0) cc_final: 0.7375 (tt0) REVERT: C 48 MET cc_start: 0.8318 (ttm) cc_final: 0.8099 (ttt) REVERT: C 104 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7444 (mm-30) REVERT: C 112 MET cc_start: 0.7900 (mmm) cc_final: 0.7692 (mmm) REVERT: D 216 LYS cc_start: 0.8074 (tttt) cc_final: 0.7251 (mttp) REVERT: E 112 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7701 (mmm) REVERT: E 140 LYS cc_start: 0.7949 (ttmp) cc_final: 0.7617 (mtmt) outliers start: 28 outliers final: 6 residues processed: 217 average time/residue: 1.3142 time to fit residues: 304.3737 Evaluate side-chains 179 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 B residue 126 GLU 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: 3.9990 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS E 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3447 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= 0.193 Angle : 0.568 14.790 14014 Z= 0.287 Chirality : 0.042 0.144 1640 Planarity : 0.004 0.037 1763 Dihedral : 5.028 21.692 1371 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.24 % Allowed : 15.08 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.94 (0.21), residues: 1312 helix: -1.29 (0.14), residues: 1081 sheet: None (None), residues: 0 loop : -0.08 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 146 HIS 0.003 0.001 HIS B 52 PHE 0.022 0.002 PHE A 121 TYR 0.015 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 213 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.152 Fit side-chains REVERT: A 23 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: A 119 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6190 (mppt) REVERT: A 122 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: A 129 GLU cc_start: 0.7299 (pt0) cc_final: 0.7085 (pt0) REVERT: A 140 LYS cc_start: 0.7882 (ttmp) cc_final: 0.7569 (ttpp) REVERT: B 48 MET cc_start: 0.8067 (ttm) cc_final: 0.7805 (ttt) REVERT: B 62 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7444 (mt-10) REVERT: B 136 GLU cc_start: 0.7614 (tt0) cc_final: 0.7378 (tt0) REVERT: C 48 MET cc_start: 0.8345 (ttm) cc_final: 0.8119 (ttt) REVERT: C 104 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7530 (mm-30) REVERT: C 140 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7395 (ttmt) REVERT: D 216 LYS cc_start: 0.8088 (tttt) cc_final: 0.7278 (mttp) REVERT: D 252 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7594 (pt) REVERT: E 140 LYS cc_start: 0.7934 (ttmp) cc_final: 0.7576 (mtmt) REVERT: E 178 MET cc_start: 0.7116 (ttp) cc_final: 0.6870 (ttp) outliers start: 35 outliers final: 8 residues processed: 198 average time/residue: 1.3931 time to fit residues: 293.6825 Evaluate side-chains 181 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 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 140 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 98 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10372 Z= 0.289 Angle : 0.604 12.646 14014 Z= 0.306 Chirality : 0.044 0.142 1640 Planarity : 0.004 0.036 1763 Dihedral : 5.056 22.086 1371 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.68 % Allowed : 16.19 % Favored : 81.13 % 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: -1.26 (0.22), residues: 1312 helix: -0.82 (0.15), residues: 1081 sheet: None (None), residues: 0 loop : 0.13 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 146 HIS 0.005 0.001 HIS A 138 PHE 0.027 0.002 PHE C 149 TYR 0.017 0.003 TYR B 145 ARG 0.003 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 196 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 0.915 Fit side-chains REVERT: A 23 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7364 (pp20) REVERT: A 119 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6220 (mppt) REVERT: A 140 LYS cc_start: 0.7943 (ttmp) cc_final: 0.7591 (ttpp) REVERT: B 48 MET cc_start: 0.8096 (ttm) cc_final: 0.7841 (ttt) REVERT: B 138 HIS cc_start: 0.7377 (t70) cc_final: 0.6610 (t-90) REVERT: C 48 MET cc_start: 0.8372 (ttm) cc_final: 0.8141 (ttt) REVERT: C 104 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7566 (mm-30) REVERT: C 140 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7466 (ttmt) REVERT: C 170 LYS cc_start: 0.7884 (mttm) cc_final: 0.7647 (mtpp) REVERT: E 140 LYS cc_start: 0.7959 (ttmp) cc_final: 0.7562 (mtmt) REVERT: E 178 MET cc_start: 0.7223 (ttp) cc_final: 0.6902 (ttp) outliers start: 29 outliers final: 12 residues processed: 185 average time/residue: 1.4512 time to fit residues: 285.0887 Evaluate side-chains 179 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 137 GLU 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: 5.9990 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS D 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3861 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= 0.169 Angle : 0.531 10.562 14014 Z= 0.269 Chirality : 0.041 0.132 1640 Planarity : 0.004 0.036 1763 Dihedral : 4.737 21.227 1371 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.41 % Allowed : 16.56 % 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: -0.62 (0.23), residues: 1312 helix: -0.33 (0.15), residues: 1091 sheet: None (None), residues: 0 loop : 0.10 (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 125 PHE 0.019 0.002 PHE A 121 TYR 0.012 0.002 TYR B 145 ARG 0.002 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 fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 1.170 Fit side-chains REVERT: A 23 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7380 (pp20) REVERT: A 37 LEU cc_start: 0.8099 (mm) cc_final: 0.7881 (mt) REVERT: A 65 VAL cc_start: 0.8862 (t) cc_final: 0.8652 (p) REVERT: A 119 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6235 (mppt) REVERT: A 140 LYS cc_start: 0.7887 (ttmp) cc_final: 0.7545 (ttpp) REVERT: A 226 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7957 (ttpp) REVERT: B 48 MET cc_start: 0.8075 (ttm) cc_final: 0.7808 (ttt) REVERT: C 48 MET cc_start: 0.8319 (ttm) cc_final: 0.8089 (ttt) REVERT: C 104 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7538 (mm-30) REVERT: E 99 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6190 (mtp180) REVERT: E 140 LYS cc_start: 0.7921 (ttmp) cc_final: 0.7549 (mtmt) REVERT: E 178 MET cc_start: 0.7142 (ttp) cc_final: 0.6833 (ttp) outliers start: 26 outliers final: 8 residues processed: 194 average time/residue: 1.3730 time to fit residues: 283.3511 Evaluate side-chains 172 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 99 ARG 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: 3.9990 chunk 112 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10372 Z= 0.220 Angle : 0.568 14.330 14014 Z= 0.285 Chirality : 0.043 0.174 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.757 21.664 1371 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.68 % Allowed : 17.58 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.23), residues: 1312 helix: -0.09 (0.15), residues: 1091 sheet: None (None), residues: 0 loop : 0.20 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 146 HIS 0.004 0.001 HIS B 52 PHE 0.021 0.002 PHE C 121 TYR 0.014 0.002 TYR B 145 ARG 0.002 0.000 ARG C 251 *********************** 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 191 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.126 Fit side-chains REVERT: A 23 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7362 (pp20) REVERT: A 37 LEU cc_start: 0.8132 (mm) cc_final: 0.7898 (mt) REVERT: A 119 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6253 (mppt) REVERT: A 140 LYS cc_start: 0.7964 (ttmp) cc_final: 0.7623 (ttpp) REVERT: B 48 MET cc_start: 0.8065 (ttm) cc_final: 0.7664 (ttt) REVERT: C 48 MET cc_start: 0.8340 (ttm) cc_final: 0.8111 (ttt) REVERT: C 104 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7534 (mm-30) REVERT: C 140 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7359 (ttmt) REVERT: C 170 LYS cc_start: 0.7827 (mttm) cc_final: 0.7554 (mtpp) REVERT: E 99 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.6302 (mtp180) REVERT: E 140 LYS cc_start: 0.7931 (ttmp) cc_final: 0.7537 (mtmt) REVERT: E 178 MET cc_start: 0.7197 (ttp) cc_final: 0.6937 (ttp) outliers start: 29 outliers final: 10 residues processed: 176 average time/residue: 1.4537 time to fit residues: 271.6807 Evaluate side-chains 173 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 99 ARG 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: 0.5980 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 138 HIS D 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4074 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= 0.158 Angle : 0.532 14.205 14014 Z= 0.265 Chirality : 0.041 0.135 1640 Planarity : 0.004 0.035 1763 Dihedral : 4.552 20.826 1371 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.04 % Allowed : 17.85 % Favored : 80.11 % 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: 0.19 (0.23), residues: 1312 helix: 0.21 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.52 (0.44), 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 125 PHE 0.018 0.001 PHE C 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 185 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 1.200 Fit side-chains REVERT: A 23 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7376 (pp20) REVERT: A 37 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 65 VAL cc_start: 0.8807 (t) cc_final: 0.8579 (p) REVERT: A 119 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6214 (mppt) REVERT: A 140 LYS cc_start: 0.7924 (ttmp) cc_final: 0.7579 (ttpp) REVERT: A 212 MET cc_start: 0.7734 (mmp) cc_final: 0.7490 (mmp) REVERT: A 226 LYS cc_start: 0.8260 (ttpt) cc_final: 0.8029 (ttpp) REVERT: B 48 MET cc_start: 0.7975 (ttm) cc_final: 0.7678 (ttt) REVERT: C 48 MET cc_start: 0.8244 (ttm) cc_final: 0.7999 (ttt) REVERT: C 104 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7529 (mm-30) REVERT: C 140 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7275 (ttmt) REVERT: C 170 LYS cc_start: 0.7765 (mttm) cc_final: 0.7514 (mtmt) REVERT: D 129 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7533 (mt-10) REVERT: E 99 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6293 (mtp180) REVERT: E 140 LYS cc_start: 0.7920 (ttmp) cc_final: 0.7544 (mtmt) REVERT: E 178 MET cc_start: 0.7026 (ttp) cc_final: 0.6690 (ttp) outliers start: 22 outliers final: 9 residues processed: 175 average time/residue: 1.4365 time to fit residues: 267.4184 Evaluate side-chains 169 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 99 ARG 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: 0.2980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.4159 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= 0.174 Angle : 0.542 13.111 14014 Z= 0.270 Chirality : 0.041 0.135 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.525 21.003 1371 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.50 % Allowed : 18.50 % 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: 0.45 (0.23), residues: 1312 helix: 0.38 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.64 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 146 HIS 0.003 0.001 HIS B 125 PHE 0.019 0.001 PHE A 121 TYR 0.012 0.002 TYR C 197 ARG 0.001 0.000 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.102 Fit side-chains REVERT: A 23 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7358 (pp20) REVERT: A 37 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7901 (mt) REVERT: A 119 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6243 (mppt) REVERT: A 140 LYS cc_start: 0.7939 (ttmp) cc_final: 0.7602 (ttpp) REVERT: A 223 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7155 (tp30) REVERT: A 226 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8008 (ttpp) REVERT: B 48 MET cc_start: 0.7993 (ttm) cc_final: 0.7688 (ttt) REVERT: B 64 LYS cc_start: 0.8376 (ptmm) cc_final: 0.8098 (ptmt) REVERT: C 48 MET cc_start: 0.8258 (ttm) cc_final: 0.8017 (ttt) REVERT: C 104 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7563 (mm-30) REVERT: C 140 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7316 (ttmt) REVERT: C 170 LYS cc_start: 0.7771 (mttm) cc_final: 0.7512 (mtmt) REVERT: D 129 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7529 (mt-10) REVERT: D 178 MET cc_start: 0.7201 (ttm) cc_final: 0.6988 (tpt) REVERT: E 99 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6495 (mtp180) REVERT: E 140 LYS cc_start: 0.7940 (ttmp) cc_final: 0.7568 (mtmt) REVERT: E 178 MET cc_start: 0.7124 (ttp) cc_final: 0.6779 (ttp) outliers start: 27 outliers final: 9 residues processed: 178 average time/residue: 1.4069 time to fit residues: 266.0624 Evaluate side-chains 171 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 99 ARG 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: 5.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.0370 chunk 104 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.4131 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= 0.213 Angle : 0.559 12.830 14014 Z= 0.279 Chirality : 0.042 0.140 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.598 21.478 1371 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.22 % Allowed : 19.70 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1312 helix: 0.39 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.66 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 146 HIS 0.003 0.001 HIS B 52 PHE 0.020 0.002 PHE C 121 TYR 0.016 0.002 TYR C 197 ARG 0.002 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 180 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 0.944 Fit side-chains REVERT: A 23 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: A 37 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7923 (mt) REVERT: A 119 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6210 (mppt) REVERT: A 140 LYS cc_start: 0.7953 (ttmp) cc_final: 0.7611 (ttpp) REVERT: A 223 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7149 (tp30) REVERT: A 226 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8028 (ttpp) REVERT: B 48 MET cc_start: 0.8013 (ttm) cc_final: 0.7704 (ttt) REVERT: B 64 LYS cc_start: 0.8371 (ptmm) cc_final: 0.8097 (ptmt) REVERT: C 48 MET cc_start: 0.8300 (ttm) cc_final: 0.8051 (ttt) REVERT: C 104 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7567 (mm-30) REVERT: C 140 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7317 (ttmt) REVERT: C 170 LYS cc_start: 0.7783 (mttm) cc_final: 0.7496 (mtmt) REVERT: D 178 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6966 (tpt) REVERT: E 99 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6349 (mtp180) REVERT: E 140 LYS cc_start: 0.7921 (ttmp) cc_final: 0.7553 (mtmt) REVERT: E 178 MET cc_start: 0.7145 (ttp) cc_final: 0.6821 (ttp) outliers start: 24 outliers final: 10 residues processed: 171 average time/residue: 1.4175 time to fit residues: 257.7304 Evaluate side-chains 169 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 99 ARG 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: 0.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.0670 chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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: 0.8162 moved from start: 0.4228 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= 0.169 Angle : 0.538 12.162 14014 Z= 0.268 Chirality : 0.041 0.135 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.498 20.807 1371 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.13 % Allowed : 20.17 % Favored : 77.71 % 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: 0.70 (0.23), residues: 1312 helix: 0.55 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.73 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 PHE 0.018 0.001 PHE C 121 TYR 0.014 0.002 TYR C 197 ARG 0.001 0.000 ARG C 251 ********************** 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 176 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.159 Fit side-chains REVERT: A 23 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7334 (pp20) REVERT: A 119 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6117 (mppt) REVERT: A 140 LYS cc_start: 0.7920 (ttmp) cc_final: 0.7583 (ttpp) REVERT: A 223 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: A 226 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7997 (ttpp) REVERT: B 48 MET cc_start: 0.7983 (ttm) cc_final: 0.7660 (ttt) REVERT: B 64 LYS cc_start: 0.8384 (ptmm) cc_final: 0.8107 (ptmt) REVERT: C 48 MET cc_start: 0.8239 (ttm) cc_final: 0.7966 (ttt) REVERT: C 104 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7568 (mm-30) REVERT: C 140 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7280 (ttmt) REVERT: C 170 LYS cc_start: 0.7776 (mttm) cc_final: 0.7484 (mtmt) REVERT: D 23 GLU cc_start: 0.7603 (tp30) cc_final: 0.7327 (tt0) REVERT: D 178 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.7041 (tpt) REVERT: E 15 SER cc_start: 0.8548 (m) cc_final: 0.8175 (t) REVERT: E 16 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6364 (mm) REVERT: E 99 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.6491 (mtp180) REVERT: E 140 LYS cc_start: 0.7901 (ttmp) cc_final: 0.7545 (mtmt) REVERT: E 178 MET cc_start: 0.7036 (ttp) cc_final: 0.6746 (ttp) outliers start: 23 outliers final: 9 residues processed: 166 average time/residue: 1.4305 time to fit residues: 252.7969 Evaluate side-chains 165 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 99 ARG 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: 1.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.136262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107933 restraints weight = 10565.006| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.46 r_work: 0.3008 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4279 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= 0.170 Angle : 0.540 11.815 14014 Z= 0.268 Chirality : 0.041 0.135 1640 Planarity : 0.004 0.034 1763 Dihedral : 4.463 20.693 1371 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.04 % Allowed : 20.63 % Favored : 77.34 % 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: 0.82 (0.23), residues: 1312 helix: 0.63 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : 0.75 (0.45), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 203 HIS 0.003 0.001 HIS B 52 PHE 0.018 0.001 PHE A 121 TYR 0.014 0.002 TYR C 197 ARG 0.001 0.000 ARG C 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4564.22 seconds wall clock time: 80 minutes 48.94 seconds (4848.94 seconds total)