Starting phenix.real_space_refine on Wed Jun 18 04:31:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k29_36835/06_2025/8k29_36835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k29_36835/06_2025/8k29_36835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k29_36835/06_2025/8k29_36835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k29_36835/06_2025/8k29_36835.map" model { file = "/net/cci-nas-00/data/ceres_data/8k29_36835/06_2025/8k29_36835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k29_36835/06_2025/8k29_36835.cif" } resolution = 3.18 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= 0.007 sd= 0.125 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: 5 Type Number sf(0) Gaussians P 127 5.49 5 S 73 5.16 5 C 12855 2.51 5 N 3587 2.21 5 O 4413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21055 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1260 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 16, 'rna3p_pur': 13, 'rna3p_pyr': 19} Link IDs: {'rna2p': 27, 'rna3p': 32} Chain: "A" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1390 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1903 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1290 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 898 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "R" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 13.31, per 1000 atoms: 0.63 Number of scatterers: 21055 At special positions: 0 Unit cell: (113.3, 140.8, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 127 15.00 O 4413 8.00 N 3587 7.00 C 12855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 19760 O5' DA Q 22 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 2.5 seconds 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 44 sheets defined 26.6% alpha, 22.1% beta 15 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 6.91 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.573A pdb=" N VAL A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.937A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.532A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.533A pdb=" N ASN B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.507A pdb=" N LEU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 149' Processing helix chain 'B' and resid 150 through 155 removed outlier: 4.493A pdb=" N ASN B 153 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.806A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.510A pdb=" N ASN C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 165 through 179 removed outlier: 3.524A pdb=" N ILE C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 284 through 298 removed outlier: 3.593A pdb=" N VAL C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.507A pdb=" N TRP D 130 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ARG D 131 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 133 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 134 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 178 removed outlier: 4.070A pdb=" N VAL D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 Processing helix chain 'D' and resid 269 through 279 removed outlier: 3.558A pdb=" N LEU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 298 Processing helix chain 'E' and resid 99 through 107 Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.841A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 removed outlier: 3.510A pdb=" N LEU E 129 " --> pdb=" O GLY E 126 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG E 131 " --> pdb=" O THR E 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 134 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.615A pdb=" N ASP E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL E 176 " --> pdb=" O MET E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.653A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 284 through 298 removed outlier: 3.567A pdb=" N PHE E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 111 through 122 Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.685A pdb=" N TRP F 130 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARG F 131 " --> pdb=" O THR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 178 removed outlier: 3.863A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL F 176 " --> pdb=" O MET F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.505A pdb=" N ARG F 234 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 280 removed outlier: 4.090A pdb=" N GLY F 276 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.866A pdb=" N PHE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 102 through 107 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.599A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY G 126 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 178 removed outlier: 3.549A pdb=" N VAL G 176 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.838A pdb=" N ASP G 275 " --> pdb=" O PHE G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 298 removed outlier: 3.703A pdb=" N PHE G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE G 296 " --> pdb=" O THR G 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.654A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE H 123 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.574A pdb=" N LEU H 129 " --> pdb=" O GLY H 126 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG H 131 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG H 133 " --> pdb=" O TRP H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 179 removed outlier: 4.163A pdb=" N MET H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 Processing helix chain 'H' and resid 269 through 280 Processing helix chain 'H' and resid 285 through 298 Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 61 through 69 removed outlier: 4.153A pdb=" N LEU I 65 " --> pdb=" O ASP I 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 109 removed outlier: 3.711A pdb=" N ARG I 103 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS I 107 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 120 removed outlier: 3.500A pdb=" N TYR I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 8.774A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 107 removed outlier: 8.774A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA B 205 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU B 190 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 207 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS B 188 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 209 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR B 186 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR B 211 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN B 180 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 142 Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.745A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.745A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA B 94 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 14 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.725A pdb=" N TYR C 12 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 21 through 26 current: chain 'C' and resid 139 through 145 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 76 through 85 current: chain 'C' and resid 217 through 218 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 45 removed outlier: 4.555A pdb=" N ALA C 68 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 235 through 237 Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.575A pdb=" N VAL C 260 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 26 current: chain 'D' and resid 139 through 144 Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 86 current: chain 'D' and resid 217 through 218 Processing sheet with id=AB9, first strand: chain 'D' and resid 40 through 45 Processing sheet with id=AC1, first strand: chain 'D' and resid 254 through 255 Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AC3, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 26 current: chain 'E' and resid 139 through 145 Processing sheet with id=AC4, first strand: chain 'E' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 76 through 86 current: chain 'E' and resid 217 through 218 Processing sheet with id=AC5, first strand: chain 'E' and resid 40 through 45 Processing sheet with id=AC6, first strand: chain 'E' and resid 235 through 237 Processing sheet with id=AC7, first strand: chain 'E' and resid 254 through 255 removed outlier: 3.515A pdb=" N VAL E 255 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AC9, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD1, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD2, first strand: chain 'F' and resid 39 through 46 Processing sheet with id=AD3, first strand: chain 'F' and resid 203 through 204 removed outlier: 4.651A pdb=" N GLN F 214 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AD5, first strand: chain 'F' and resid 235 through 237 Processing sheet with id=AD6, first strand: chain 'F' and resid 254 through 255 removed outlier: 3.642A pdb=" N VAL F 260 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.024A pdb=" N GLY G 299 " --> pdb=" O TYR G 12 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 26 current: chain 'G' and resid 139 through 144 Processing sheet with id=AD9, first strand: chain 'G' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 76 through 86 current: chain 'G' and resid 217 through 218 Processing sheet with id=AE1, first strand: chain 'G' and resid 39 through 44 removed outlier: 4.462A pdb=" N ALA G 68 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 254 through 255 removed outlier: 3.582A pdb=" N VAL G 260 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE4, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.568A pdb=" N MET H 191 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 145 " --> pdb=" O GLN H 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.580A pdb=" N MET H 224 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA H 222 " --> pdb=" O MET H 23 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 40 through 44 removed outlier: 3.867A pdb=" N GLY H 40 " --> pdb=" O PHE H 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 39 through 40 removed outlier: 5.999A pdb=" N THR I 3 " --> pdb=" O PRO I 81 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER I 5 " --> pdb=" O GLY I 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 90 through 93 removed outlier: 3.837A pdb=" N PHE I 147 " --> pdb=" O VAL I 93 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 6.61 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3338 1.30 - 1.43: 6164 1.43 - 1.56: 11796 1.56 - 1.69: 261 1.69 - 1.82: 131 Bond restraints: 21690 Sorted by residual: bond pdb=" CA LYS G 91 " pdb=" C LYS G 91 " ideal model delta sigma weight residual 1.523 1.414 0.108 1.23e-02 6.61e+03 7.77e+01 bond pdb=" CA ASP G 226 " pdb=" C ASP G 226 " ideal model delta sigma weight residual 1.522 1.419 0.104 1.37e-02 5.33e+03 5.71e+01 bond pdb=" CA THR A 99 " pdb=" C THR A 99 " ideal model delta sigma weight residual 1.525 1.442 0.083 1.32e-02 5.74e+03 3.96e+01 bond pdb=" CA LYS G 228 " pdb=" C LYS G 228 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.29e-02 6.01e+03 3.56e+01 bond pdb=" CA HIS G 225 " pdb=" C HIS G 225 " ideal model delta sigma weight residual 1.527 1.452 0.075 1.34e-02 5.57e+03 3.10e+01 ... (remaining 21685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 29383 3.36 - 6.72: 493 6.72 - 10.09: 80 10.09 - 13.45: 11 13.45 - 16.81: 3 Bond angle restraints: 29970 Sorted by residual: angle pdb=" N SER B 150 " pdb=" CA SER B 150 " pdb=" C SER B 150 " ideal model delta sigma weight residual 113.61 96.80 16.81 1.50e+00 4.44e-01 1.26e+02 angle pdb=" N TRP H 239 " pdb=" CA TRP H 239 " pdb=" C TRP H 239 " ideal model delta sigma weight residual 112.92 99.43 13.49 1.23e+00 6.61e-01 1.20e+02 angle pdb=" N LYS B 116 " pdb=" CA LYS B 116 " pdb=" C LYS B 116 " ideal model delta sigma weight residual 113.02 99.94 13.08 1.20e+00 6.94e-01 1.19e+02 angle pdb=" O3' A P 36 " pdb=" C3' A P 36 " pdb=" C2' A P 36 " ideal model delta sigma weight residual 109.50 122.55 -13.05 1.50e+00 4.44e-01 7.57e+01 angle pdb=" C4' DA Q 52 " pdb=" C3' DA Q 52 " pdb=" O3' DA Q 52 " ideal model delta sigma weight residual 110.00 122.78 -12.78 1.50e+00 4.44e-01 7.26e+01 ... (remaining 29965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 11727 34.35 - 68.69: 938 68.69 - 103.04: 68 103.04 - 137.38: 3 137.38 - 171.73: 9 Dihedral angle restraints: 12745 sinusoidal: 5899 harmonic: 6846 Sorted by residual: dihedral pdb=" C MET B 156 " pdb=" N MET B 156 " pdb=" CA MET B 156 " pdb=" CB MET B 156 " ideal model delta harmonic sigma weight residual -122.60 -154.82 32.22 0 2.50e+00 1.60e-01 1.66e+02 dihedral pdb=" N MET B 156 " pdb=" C MET B 156 " pdb=" CA MET B 156 " pdb=" CB MET B 156 " ideal model delta harmonic sigma weight residual 122.80 152.44 -29.64 0 2.50e+00 1.60e-01 1.41e+02 dihedral pdb=" O4' C P 44 " pdb=" C1' C P 44 " pdb=" N1 C P 44 " pdb=" C2 C P 44 " ideal model delta sinusoidal sigma weight residual 200.00 38.95 161.05 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 12742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 3452 0.282 - 0.564: 17 0.564 - 0.847: 4 0.847 - 1.129: 0 1.129 - 1.411: 1 Chirality restraints: 3474 Sorted by residual: chirality pdb=" CA MET B 156 " pdb=" N MET B 156 " pdb=" C MET B 156 " pdb=" CB MET B 156 " both_signs ideal model delta sigma weight residual False 2.51 1.10 1.41 2.00e-01 2.50e+01 4.98e+01 chirality pdb=" CB VAL C 183 " pdb=" CA VAL C 183 " pdb=" CG1 VAL C 183 " pdb=" CG2 VAL C 183 " both_signs ideal model delta sigma weight residual False -2.63 -1.95 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C3' A P 36 " pdb=" C4' A P 36 " pdb=" O3' A P 36 " pdb=" C2' A P 36 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 3471 not shown) Planarity restraints: 3433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 156 " 0.095 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 157 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 154 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C ALA B 154 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA B 154 " 0.029 2.00e-02 2.50e+03 pdb=" N MET B 155 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 196 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C LYS B 196 " 0.066 2.00e-02 2.50e+03 pdb=" O LYS B 196 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS B 197 " -0.022 2.00e-02 2.50e+03 ... (remaining 3430 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 25 1.89 - 2.65: 539 2.65 - 3.40: 27604 3.40 - 4.15: 58262 4.15 - 4.90: 98954 Nonbonded interactions: 185384 Sorted by model distance: nonbonded pdb=" ND2 ASN G 61 " pdb=" C5' DA Q 22 " model vdw 1.142 3.520 nonbonded pdb=" OD1 ASN B 222 " pdb=" OP1 DA R 37 " model vdw 1.181 3.040 nonbonded pdb=" C2 A P 31 " pdb=" C5 DC Q 20 " model vdw 1.244 3.640 nonbonded pdb=" N1 A P 31 " pdb=" N4 DC Q 20 " model vdw 1.246 3.200 nonbonded pdb=" N1 A P 31 " pdb=" C4 DC Q 20 " model vdw 1.355 3.340 ... (remaining 185379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 50.480 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.007 0.108 21691 Z= 0.402 Angle : 1.120 16.808 29972 Z= 0.680 Chirality : 0.071 1.411 3474 Planarity : 0.007 0.142 3433 Dihedral : 22.140 171.731 8368 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.68 % Favored : 92.77 % Rotamer: Outliers : 2.60 % Allowed : 27.83 % Favored : 69.57 % Cbeta Deviations : 0.14 % 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: -3.09 (0.15), residues: 2379 helix: -2.54 (0.16), residues: 658 sheet: -0.82 (0.24), residues: 438 loop : -2.24 (0.15), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 28 HIS 0.020 0.002 HIS G 225 PHE 0.044 0.002 PHE G 150 TYR 0.045 0.003 TYR H 81 ARG 0.012 0.001 ARG G 133 Details of bonding type rmsd hydrogen bonds : bond 0.24377 ( 638) hydrogen bonds : angle 9.60641 ( 1760) SS BOND : bond 0.00313 ( 1) SS BOND : angle 2.55612 ( 2) covalent geometry : bond 0.00663 (21690) covalent geometry : angle 1.11960 (29970) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 395 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.7018 (mm) cc_final: 0.6737 (mm) REVERT: A 137 TYR cc_start: 0.8286 (m-10) cc_final: 0.8048 (m-10) REVERT: A 158 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7701 (mmmt) REVERT: A 159 MET cc_start: 0.8573 (mtp) cc_final: 0.8245 (mtp) REVERT: B 26 MET cc_start: 0.8717 (tpt) cc_final: 0.8184 (tpt) REVERT: B 108 ASP cc_start: 0.8457 (m-30) cc_final: 0.8248 (m-30) REVERT: B 146 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: B 155 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8274 (ptm) REVERT: B 172 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: B 197 HIS cc_start: 0.7781 (m170) cc_final: 0.7474 (m90) REVERT: B 214 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7765 (mtm) REVERT: C 38 MET cc_start: 0.7775 (mmm) cc_final: 0.7412 (mmp) REVERT: C 191 MET cc_start: 0.8220 (mtm) cc_final: 0.8009 (mtm) REVERT: C 224 MET cc_start: 0.8468 (mtp) cc_final: 0.8264 (mtp) REVERT: D 5 LYS cc_start: 0.7848 (mppt) cc_final: 0.7556 (mmtm) REVERT: D 217 ASP cc_start: 0.7005 (p0) cc_final: 0.6750 (p0) REVERT: E 204 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7389 (mt-10) REVERT: E 289 MET cc_start: 0.8424 (mtm) cc_final: 0.8219 (mtm) REVERT: F 117 TYR cc_start: 0.6839 (t80) cc_final: 0.6223 (t80) REVERT: F 148 GLN cc_start: 0.7991 (pt0) cc_final: 0.7658 (pt0) REVERT: F 172 MET cc_start: 0.8561 (mtt) cc_final: 0.8361 (mtt) REVERT: G 63 GLN cc_start: 0.5462 (pm20) cc_final: 0.5077 (pm20) REVERT: G 200 PHE cc_start: 0.7796 (m-80) cc_final: 0.7536 (m-80) REVERT: H 156 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.6539 (tt) outliers start: 51 outliers final: 10 residues processed: 423 average time/residue: 0.3278 time to fit residues: 217.7911 Evaluate side-chains 281 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 265 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 226 optimal weight: 0.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN D 63 GLN D 109 ASN D 227 GLN E 61 ASN E 63 GLN E 146 ASN F 61 ASN F 63 GLN G 258 ASN H 189 HIS H 214 GLN I 47 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120375 restraints weight = 29770.505| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.96 r_work: 0.3228 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21691 Z= 0.163 Angle : 0.643 7.922 29972 Z= 0.357 Chirality : 0.044 0.277 3474 Planarity : 0.006 0.133 3433 Dihedral : 21.568 179.931 4261 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.25 % Favored : 94.49 % Rotamer: Outliers : 3.47 % Allowed : 25.43 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -2.58 (0.16), residues: 2379 helix: -1.84 (0.17), residues: 682 sheet: -0.87 (0.24), residues: 475 loop : -1.96 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 239 HIS 0.006 0.001 HIS A 134 PHE 0.022 0.001 PHE B 64 TYR 0.021 0.001 TYR H 117 ARG 0.005 0.001 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 638) hydrogen bonds : angle 6.02645 ( 1760) SS BOND : bond 0.00258 ( 1) SS BOND : angle 2.26498 ( 2) covalent geometry : bond 0.00348 (21690) covalent geometry : angle 0.64268 (29970) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 301 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8681 (m-10) cc_final: 0.8389 (m-10) REVERT: A 158 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8075 (mmmt) REVERT: B 26 MET cc_start: 0.9013 (tpt) cc_final: 0.8717 (tpt) REVERT: B 115 ASP cc_start: 0.8700 (m-30) cc_final: 0.8260 (p0) REVERT: B 202 PHE cc_start: 0.8366 (p90) cc_final: 0.8156 (p90) REVERT: B 213 THR cc_start: 0.8934 (t) cc_final: 0.8695 (t) REVERT: B 214 MET cc_start: 0.8835 (mmm) cc_final: 0.8393 (mmm) REVERT: C 191 MET cc_start: 0.8762 (mtm) cc_final: 0.8532 (mtm) REVERT: C 275 ASP cc_start: 0.8227 (m-30) cc_final: 0.7404 (m-30) REVERT: D 5 LYS cc_start: 0.8027 (mppt) cc_final: 0.7659 (mmtm) REVERT: D 217 ASP cc_start: 0.7940 (p0) cc_final: 0.7683 (p0) REVERT: E 204 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7873 (mt-10) REVERT: F 99 TYR cc_start: 0.8906 (t80) cc_final: 0.8642 (t80) REVERT: F 162 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7809 (tp30) REVERT: H 78 LEU cc_start: 0.7438 (tp) cc_final: 0.7129 (tp) outliers start: 68 outliers final: 27 residues processed: 347 average time/residue: 0.3062 time to fit residues: 168.8483 Evaluate side-chains 281 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 239 TRP Chi-restraints excluded: chain I residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 60 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 179 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 180 GLN E 17 ASN F 63 GLN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.115577 restraints weight = 29121.062| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.86 r_work: 0.3167 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21691 Z= 0.182 Angle : 0.612 8.694 29972 Z= 0.337 Chirality : 0.044 0.247 3474 Planarity : 0.005 0.135 3433 Dihedral : 21.284 178.274 4233 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.92 % Favored : 94.87 % Rotamer: Outliers : 3.41 % Allowed : 25.48 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -2.11 (0.16), residues: 2379 helix: -1.15 (0.19), residues: 653 sheet: -0.86 (0.24), residues: 450 loop : -1.73 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 239 HIS 0.005 0.001 HIS F 72 PHE 0.016 0.001 PHE B 64 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 638) hydrogen bonds : angle 5.43322 ( 1760) SS BOND : bond 0.00177 ( 1) SS BOND : angle 1.60705 ( 2) covalent geometry : bond 0.00400 (21690) covalent geometry : angle 0.61192 (29970) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 261 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7873 (t0) cc_final: 0.7385 (t0) REVERT: A 137 TYR cc_start: 0.8779 (m-10) cc_final: 0.8463 (m-10) REVERT: B 26 MET cc_start: 0.9148 (tpt) cc_final: 0.8891 (tpt) REVERT: B 62 SER cc_start: 0.8800 (t) cc_final: 0.8497 (p) REVERT: B 115 ASP cc_start: 0.8587 (m-30) cc_final: 0.7807 (t0) REVERT: C 5 LYS cc_start: 0.6263 (tmtt) cc_final: 0.5956 (tmtt) REVERT: C 121 TYR cc_start: 0.8973 (t80) cc_final: 0.8194 (t80) REVERT: D 5 LYS cc_start: 0.8120 (mppt) cc_final: 0.7720 (mmtm) REVERT: D 38 MET cc_start: 0.8885 (mmt) cc_final: 0.8550 (mmt) REVERT: E 156 LEU cc_start: 0.8257 (mp) cc_final: 0.7971 (mt) REVERT: F 9 VAL cc_start: 0.8298 (t) cc_final: 0.8049 (p) REVERT: F 99 TYR cc_start: 0.8932 (t80) cc_final: 0.8620 (t80) REVERT: G 235 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8085 (p) REVERT: G 262 TYR cc_start: 0.8817 (m-80) cc_final: 0.8328 (m-80) REVERT: H 38 MET cc_start: 0.7691 (mmm) cc_final: 0.7137 (mmm) REVERT: H 224 MET cc_start: 0.8286 (tpt) cc_final: 0.7960 (tpp) REVERT: I 135 VAL cc_start: 0.5774 (OUTLIER) cc_final: 0.5354 (t) outliers start: 67 outliers final: 36 residues processed: 306 average time/residue: 0.3145 time to fit residues: 151.4853 Evaluate side-chains 281 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Chi-restraints excluded: chain I residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 239 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN D 63 GLN D 158 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN G 203 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113354 restraints weight = 29257.943| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.93 r_work: 0.3125 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21691 Z= 0.200 Angle : 0.611 8.595 29972 Z= 0.333 Chirality : 0.044 0.284 3474 Planarity : 0.005 0.138 3433 Dihedral : 21.253 179.009 4225 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.72 % Favored : 94.07 % Rotamer: Outliers : 4.03 % Allowed : 24.72 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.93 (0.16), residues: 2379 helix: -0.86 (0.19), residues: 648 sheet: -0.86 (0.24), residues: 449 loop : -1.65 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 239 HIS 0.005 0.001 HIS B 197 PHE 0.012 0.001 PHE B 64 TYR 0.014 0.001 TYR H 117 ARG 0.005 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 638) hydrogen bonds : angle 5.24341 ( 1760) SS BOND : bond 0.00389 ( 1) SS BOND : angle 3.15866 ( 2) covalent geometry : bond 0.00445 (21690) covalent geometry : angle 0.61023 (29970) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 254 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 TYR cc_start: 0.8005 (t80) cc_final: 0.7800 (t80) REVERT: A 137 TYR cc_start: 0.8879 (m-10) cc_final: 0.8555 (m-10) REVERT: B 26 MET cc_start: 0.9183 (tpt) cc_final: 0.8793 (tpt) REVERT: B 62 SER cc_start: 0.8823 (t) cc_final: 0.8588 (p) REVERT: B 115 ASP cc_start: 0.8515 (m-30) cc_final: 0.7850 (t0) REVERT: B 182 MET cc_start: 0.8572 (ttp) cc_final: 0.8199 (ttp) REVERT: C 5 LYS cc_start: 0.6361 (tmtt) cc_final: 0.5957 (tmtt) REVERT: C 121 TYR cc_start: 0.8985 (t80) cc_final: 0.8185 (t80) REVERT: C 183 VAL cc_start: 0.8852 (m) cc_final: 0.8544 (p) REVERT: C 191 MET cc_start: 0.8824 (mtm) cc_final: 0.8563 (mtm) REVERT: C 275 ASP cc_start: 0.8062 (m-30) cc_final: 0.7585 (m-30) REVERT: D 5 LYS cc_start: 0.8174 (mppt) cc_final: 0.7802 (mmtm) REVERT: D 257 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8103 (mtt90) REVERT: E 156 LEU cc_start: 0.8193 (mp) cc_final: 0.7892 (mt) REVERT: F 9 VAL cc_start: 0.8397 (t) cc_final: 0.8152 (p) REVERT: F 99 TYR cc_start: 0.8985 (t80) cc_final: 0.8735 (t80) REVERT: G 235 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8038 (p) REVERT: G 262 TYR cc_start: 0.8923 (m-80) cc_final: 0.8529 (m-80) REVERT: H 38 MET cc_start: 0.7724 (mmm) cc_final: 0.7153 (mmm) REVERT: H 118 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7145 (ttm170) REVERT: H 224 MET cc_start: 0.8385 (tpt) cc_final: 0.8131 (tpp) outliers start: 79 outliers final: 45 residues processed: 310 average time/residue: 0.3058 time to fit residues: 149.2779 Evaluate side-chains 287 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 235 optimal weight: 30.0000 chunk 187 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 201 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 147 optimal weight: 0.0270 chunk 230 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 158 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.156575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113426 restraints weight = 29288.597| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.82 r_work: 0.3114 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21691 Z= 0.211 Angle : 0.610 9.341 29972 Z= 0.332 Chirality : 0.044 0.250 3474 Planarity : 0.005 0.135 3433 Dihedral : 21.235 179.166 4225 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.63 % Favored : 94.16 % Rotamer: Outliers : 3.62 % Allowed : 25.08 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.76 (0.16), residues: 2379 helix: -0.67 (0.19), residues: 644 sheet: -0.58 (0.26), residues: 401 loop : -1.62 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 239 HIS 0.006 0.001 HIS B 197 PHE 0.021 0.001 PHE B 202 TYR 0.014 0.001 TYR H 117 ARG 0.007 0.000 ARG G 133 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 638) hydrogen bonds : angle 5.19544 ( 1760) SS BOND : bond 0.00227 ( 1) SS BOND : angle 2.63852 ( 2) covalent geometry : bond 0.00469 (21690) covalent geometry : angle 0.60959 (29970) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 249 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8824 (m-10) cc_final: 0.8459 (m-10) REVERT: B 26 MET cc_start: 0.9127 (tpt) cc_final: 0.8762 (tpt) REVERT: B 62 SER cc_start: 0.8804 (t) cc_final: 0.8528 (p) REVERT: B 108 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: B 115 ASP cc_start: 0.8406 (m-30) cc_final: 0.7921 (t0) REVERT: B 182 MET cc_start: 0.8603 (ttp) cc_final: 0.8397 (ttp) REVERT: C 5 LYS cc_start: 0.6627 (tmtt) cc_final: 0.6153 (tmtt) REVERT: C 121 TYR cc_start: 0.8939 (t80) cc_final: 0.8181 (t80) REVERT: C 183 VAL cc_start: 0.8894 (m) cc_final: 0.8646 (p) REVERT: C 275 ASP cc_start: 0.8073 (m-30) cc_final: 0.7644 (m-30) REVERT: D 5 LYS cc_start: 0.8134 (mppt) cc_final: 0.7875 (mmtm) REVERT: D 227 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: F 9 VAL cc_start: 0.8329 (t) cc_final: 0.8120 (p) REVERT: F 162 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7362 (mp0) REVERT: G 191 MET cc_start: 0.8659 (pmm) cc_final: 0.8248 (ptp) REVERT: G 235 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8170 (p) REVERT: G 262 TYR cc_start: 0.8942 (m-80) cc_final: 0.8709 (m-80) REVERT: H 38 MET cc_start: 0.7725 (mmm) cc_final: 0.7114 (mmm) REVERT: H 118 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.7125 (ttm170) outliers start: 71 outliers final: 50 residues processed: 300 average time/residue: 0.2872 time to fit residues: 138.3921 Evaluate side-chains 291 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 172 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 42 optimal weight: 7.9990 chunk 202 optimal weight: 0.0010 chunk 17 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 220 optimal weight: 0.0870 chunk 174 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 201 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 overall best weight: 0.7568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN B 84 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN D 158 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 GLN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.159481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.116922 restraints weight = 29098.352| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.72 r_work: 0.3178 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21691 Z= 0.140 Angle : 0.567 9.265 29972 Z= 0.308 Chirality : 0.042 0.235 3474 Planarity : 0.005 0.132 3433 Dihedral : 21.188 179.978 4225 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.25 % Favored : 94.54 % Rotamer: Outliers : 3.26 % Allowed : 26.25 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.56 (0.16), residues: 2379 helix: -0.43 (0.20), residues: 644 sheet: -0.50 (0.26), residues: 401 loop : -1.53 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 PHE 0.024 0.001 PHE B 202 TYR 0.015 0.001 TYR H 117 ARG 0.006 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 638) hydrogen bonds : angle 4.96521 ( 1760) SS BOND : bond 0.00552 ( 1) SS BOND : angle 3.86953 ( 2) covalent geometry : bond 0.00309 (21690) covalent geometry : angle 0.56661 (29970) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 257 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7864 (t0) cc_final: 0.7591 (t0) REVERT: A 137 TYR cc_start: 0.8734 (m-10) cc_final: 0.8364 (m-10) REVERT: B 26 MET cc_start: 0.9073 (tpt) cc_final: 0.8833 (tpt) REVERT: B 108 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: B 115 ASP cc_start: 0.8295 (m-30) cc_final: 0.7905 (t0) REVERT: B 156 MET cc_start: 0.7543 (tpt) cc_final: 0.7273 (tpt) REVERT: B 182 MET cc_start: 0.8682 (ttp) cc_final: 0.8220 (ttp) REVERT: C 121 TYR cc_start: 0.8876 (t80) cc_final: 0.8121 (t80) REVERT: C 183 VAL cc_start: 0.8648 (m) cc_final: 0.8375 (p) REVERT: C 275 ASP cc_start: 0.8008 (m-30) cc_final: 0.7614 (m-30) REVERT: D 5 LYS cc_start: 0.8058 (mppt) cc_final: 0.7812 (mmtm) REVERT: D 227 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: E 117 TYR cc_start: 0.8655 (t80) cc_final: 0.8452 (t80) REVERT: G 156 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8220 (mm) REVERT: G 191 MET cc_start: 0.8650 (pmm) cc_final: 0.8218 (ptp) REVERT: G 235 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8064 (p) REVERT: G 262 TYR cc_start: 0.8864 (m-80) cc_final: 0.8663 (m-80) REVERT: H 38 MET cc_start: 0.7713 (mmm) cc_final: 0.7112 (mmm) REVERT: H 169 ILE cc_start: 0.6697 (tt) cc_final: 0.5818 (mt) outliers start: 64 outliers final: 47 residues processed: 303 average time/residue: 0.2872 time to fit residues: 139.8334 Evaluate side-chains 291 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 30 optimal weight: 1.9990 chunk 200 optimal weight: 30.0000 chunk 239 optimal weight: 7.9990 chunk 6 optimal weight: 0.1980 chunk 205 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 235 optimal weight: 40.0000 chunk 65 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN D 158 ASN F 33 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115619 restraints weight = 29051.742| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.76 r_work: 0.3150 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21691 Z= 0.165 Angle : 0.580 9.290 29972 Z= 0.315 Chirality : 0.042 0.224 3474 Planarity : 0.005 0.130 3433 Dihedral : 21.162 179.841 4225 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.38 % Favored : 94.41 % Rotamer: Outliers : 3.52 % Allowed : 26.04 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.47 (0.17), residues: 2379 helix: -0.36 (0.20), residues: 647 sheet: -0.63 (0.25), residues: 431 loop : -1.41 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 PHE 0.026 0.001 PHE B 202 TYR 0.014 0.001 TYR H 117 ARG 0.005 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 638) hydrogen bonds : angle 4.94034 ( 1760) SS BOND : bond 0.00172 ( 1) SS BOND : angle 3.21114 ( 2) covalent geometry : bond 0.00370 (21690) covalent geometry : angle 0.57961 (29970) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 248 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7860 (t0) cc_final: 0.7623 (t0) REVERT: A 137 TYR cc_start: 0.8722 (m-10) cc_final: 0.8351 (m-10) REVERT: B 26 MET cc_start: 0.9081 (tpt) cc_final: 0.8843 (tpt) REVERT: B 108 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: B 115 ASP cc_start: 0.8281 (m-30) cc_final: 0.7906 (t0) REVERT: B 179 LEU cc_start: 0.7973 (tp) cc_final: 0.7728 (mt) REVERT: B 182 MET cc_start: 0.8641 (ttp) cc_final: 0.8132 (ttp) REVERT: C 121 TYR cc_start: 0.8899 (t80) cc_final: 0.8122 (t80) REVERT: C 183 VAL cc_start: 0.8814 (m) cc_final: 0.8569 (p) REVERT: C 275 ASP cc_start: 0.8032 (m-30) cc_final: 0.7664 (m-30) REVERT: D 5 LYS cc_start: 0.8105 (mppt) cc_final: 0.7865 (mmtm) REVERT: D 38 MET cc_start: 0.8721 (mmt) cc_final: 0.8296 (mmp) REVERT: D 257 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7997 (mtt90) REVERT: F 9 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7907 (p) REVERT: F 33 ASN cc_start: 0.8128 (m110) cc_final: 0.7811 (p0) REVERT: G 191 MET cc_start: 0.8667 (pmm) cc_final: 0.8338 (ptp) REVERT: G 235 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (p) REVERT: H 38 MET cc_start: 0.7707 (mmm) cc_final: 0.7091 (mmm) REVERT: H 118 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7150 (ttm170) REVERT: H 119 TYR cc_start: 0.7818 (m-10) cc_final: 0.7567 (m-10) REVERT: H 169 ILE cc_start: 0.6724 (tt) cc_final: 0.5920 (mt) REVERT: H 263 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7747 (mtt-85) outliers start: 69 outliers final: 52 residues processed: 296 average time/residue: 0.2922 time to fit residues: 140.3112 Evaluate side-chains 296 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 241 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 119 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN D 158 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117247 restraints weight = 29231.718| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.82 r_work: 0.3167 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21691 Z= 0.139 Angle : 0.563 9.588 29972 Z= 0.305 Chirality : 0.041 0.221 3474 Planarity : 0.004 0.127 3433 Dihedral : 21.141 179.272 4225 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 3.16 % Allowed : 26.45 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.33 (0.17), residues: 2379 helix: -0.23 (0.20), residues: 646 sheet: -0.58 (0.26), residues: 431 loop : -1.31 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 239 HIS 0.004 0.001 HIS B 197 PHE 0.026 0.001 PHE B 202 TYR 0.014 0.001 TYR H 117 ARG 0.005 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 638) hydrogen bonds : angle 4.85272 ( 1760) SS BOND : bond 0.00186 ( 1) SS BOND : angle 2.66168 ( 2) covalent geometry : bond 0.00311 (21690) covalent geometry : angle 0.56259 (29970) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7793 (t0) cc_final: 0.7502 (t0) REVERT: A 137 TYR cc_start: 0.8580 (m-10) cc_final: 0.8121 (m-10) REVERT: B 26 MET cc_start: 0.9075 (tpt) cc_final: 0.8793 (tpt) REVERT: B 108 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8177 (m-30) REVERT: B 115 ASP cc_start: 0.8329 (m-30) cc_final: 0.7978 (t0) REVERT: B 179 LEU cc_start: 0.7857 (tp) cc_final: 0.7631 (mt) REVERT: B 182 MET cc_start: 0.8673 (ttp) cc_final: 0.8180 (ttp) REVERT: C 121 TYR cc_start: 0.8880 (t80) cc_final: 0.8109 (t80) REVERT: C 183 VAL cc_start: 0.8627 (m) cc_final: 0.8370 (p) REVERT: C 275 ASP cc_start: 0.8095 (m-30) cc_final: 0.7780 (m-30) REVERT: C 301 PHE cc_start: 0.8228 (m-10) cc_final: 0.7777 (m-10) REVERT: D 5 LYS cc_start: 0.8085 (mppt) cc_final: 0.7842 (mmtm) REVERT: D 38 MET cc_start: 0.8668 (mmt) cc_final: 0.8261 (mmp) REVERT: D 227 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: D 257 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7950 (mtt90) REVERT: E 117 TYR cc_start: 0.8656 (t80) cc_final: 0.8395 (t80) REVERT: E 202 SER cc_start: 0.9020 (p) cc_final: 0.8795 (p) REVERT: F 33 ASN cc_start: 0.8205 (m110) cc_final: 0.7873 (p0) REVERT: F 148 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: G 235 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8147 (p) REVERT: H 38 MET cc_start: 0.7575 (mmm) cc_final: 0.6988 (mmm) REVERT: H 119 TYR cc_start: 0.7790 (m-10) cc_final: 0.7575 (m-10) REVERT: H 169 ILE cc_start: 0.6678 (tt) cc_final: 0.6342 (tp) REVERT: H 263 ARG cc_start: 0.8133 (mtp85) cc_final: 0.7692 (mtt-85) outliers start: 62 outliers final: 52 residues processed: 291 average time/residue: 0.3190 time to fit residues: 149.2120 Evaluate side-chains 296 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 215 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 199 optimal weight: 8.9990 chunk 165 optimal weight: 0.0070 chunk 30 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 172 optimal weight: 0.0470 chunk 224 optimal weight: 1.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 16 ASN B 135 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.159250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116912 restraints weight = 29189.941| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.82 r_work: 0.3164 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21691 Z= 0.151 Angle : 0.575 9.695 29972 Z= 0.310 Chirality : 0.042 0.220 3474 Planarity : 0.004 0.127 3433 Dihedral : 21.116 179.081 4225 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.17 % Favored : 94.66 % Rotamer: Outliers : 3.52 % Allowed : 25.94 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.29 (0.17), residues: 2379 helix: -0.20 (0.20), residues: 646 sheet: -0.53 (0.26), residues: 425 loop : -1.30 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 PHE 0.027 0.001 PHE B 202 TYR 0.023 0.001 TYR H 81 ARG 0.006 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 638) hydrogen bonds : angle 4.84866 ( 1760) SS BOND : bond 0.01033 ( 1) SS BOND : angle 4.66946 ( 2) covalent geometry : bond 0.00337 (21690) covalent geometry : angle 0.57334 (29970) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 242 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7820 (t0) cc_final: 0.7593 (t0) REVERT: B 26 MET cc_start: 0.9064 (tpt) cc_final: 0.8787 (tpt) REVERT: B 108 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: B 115 ASP cc_start: 0.8362 (m-30) cc_final: 0.7999 (t0) REVERT: B 179 LEU cc_start: 0.7879 (tp) cc_final: 0.7645 (mt) REVERT: B 182 MET cc_start: 0.8676 (ttp) cc_final: 0.8176 (ttp) REVERT: C 121 TYR cc_start: 0.8885 (t80) cc_final: 0.8111 (t80) REVERT: C 183 VAL cc_start: 0.8736 (m) cc_final: 0.8455 (p) REVERT: C 275 ASP cc_start: 0.8070 (m-30) cc_final: 0.7762 (m-30) REVERT: C 301 PHE cc_start: 0.8184 (m-10) cc_final: 0.7749 (m-10) REVERT: D 5 LYS cc_start: 0.8064 (mppt) cc_final: 0.7829 (mmtm) REVERT: D 38 MET cc_start: 0.8680 (mmt) cc_final: 0.8284 (mmp) REVERT: D 227 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: E 117 TYR cc_start: 0.8719 (t80) cc_final: 0.8463 (t80) REVERT: F 9 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7782 (p) REVERT: F 148 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: G 235 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8136 (p) REVERT: G 262 TYR cc_start: 0.8911 (m-80) cc_final: 0.8670 (m-80) REVERT: H 38 MET cc_start: 0.7544 (mmm) cc_final: 0.6949 (mmm) REVERT: H 119 TYR cc_start: 0.7740 (m-10) cc_final: 0.7536 (m-10) REVERT: H 169 ILE cc_start: 0.6759 (tt) cc_final: 0.6460 (tp) outliers start: 69 outliers final: 56 residues processed: 292 average time/residue: 0.3021 time to fit residues: 143.0284 Evaluate side-chains 296 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 197 HIS Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 231 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 16 ASN B 135 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115346 restraints weight = 29233.617| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.82 r_work: 0.3146 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21691 Z= 0.171 Angle : 0.587 9.781 29972 Z= 0.315 Chirality : 0.042 0.219 3474 Planarity : 0.004 0.126 3433 Dihedral : 21.120 178.906 4225 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 3.01 % Allowed : 26.66 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.30 (0.17), residues: 2379 helix: -0.24 (0.20), residues: 644 sheet: -0.58 (0.25), residues: 433 loop : -1.26 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 239 HIS 0.006 0.001 HIS B 197 PHE 0.028 0.001 PHE B 202 TYR 0.023 0.001 TYR H 81 ARG 0.013 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 638) hydrogen bonds : angle 4.87604 ( 1760) SS BOND : bond 0.00773 ( 1) SS BOND : angle 4.55389 ( 2) covalent geometry : bond 0.00384 (21690) covalent geometry : angle 0.58536 (29970) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7893 (t0) cc_final: 0.7627 (t0) REVERT: B 26 MET cc_start: 0.9085 (tpt) cc_final: 0.8758 (tpt) REVERT: B 108 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8221 (m-30) REVERT: B 115 ASP cc_start: 0.8319 (m-30) cc_final: 0.8000 (t0) REVERT: B 179 LEU cc_start: 0.7929 (tp) cc_final: 0.7718 (mt) REVERT: B 182 MET cc_start: 0.8681 (ttp) cc_final: 0.8172 (ttp) REVERT: C 121 TYR cc_start: 0.8887 (t80) cc_final: 0.8175 (t80) REVERT: C 183 VAL cc_start: 0.8801 (m) cc_final: 0.8533 (p) REVERT: D 5 LYS cc_start: 0.8082 (mppt) cc_final: 0.7855 (mmtm) REVERT: D 227 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8356 (pt0) REVERT: D 257 ARG cc_start: 0.8387 (mtp85) cc_final: 0.8017 (mtt90) REVERT: F 9 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7861 (p) REVERT: F 148 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: G 235 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8136 (p) REVERT: G 262 TYR cc_start: 0.8930 (m-80) cc_final: 0.8705 (m-80) REVERT: H 119 TYR cc_start: 0.7772 (m-10) cc_final: 0.7564 (m-10) REVERT: H 133 ARG cc_start: 0.6283 (ttp80) cc_final: 0.6078 (ptt-90) REVERT: H 169 ILE cc_start: 0.6798 (tt) cc_final: 0.6461 (tp) REVERT: H 263 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7122 (mtt180) outliers start: 59 outliers final: 54 residues processed: 285 average time/residue: 0.3229 time to fit residues: 145.3178 Evaluate side-chains 291 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 284 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 23 MET Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 75 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 44 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 69 optimal weight: 0.5980 chunk 211 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 0.0770 chunk 92 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 ASN B 16 ASN B 135 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118386 restraints weight = 29261.344| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.78 r_work: 0.3187 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21691 Z= 0.129 Angle : 0.569 9.806 29972 Z= 0.307 Chirality : 0.041 0.218 3474 Planarity : 0.004 0.125 3433 Dihedral : 21.124 178.301 4225 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 2.91 % Allowed : 26.96 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -1.25 (0.17), residues: 2379 helix: -0.12 (0.20), residues: 628 sheet: -0.65 (0.26), residues: 426 loop : -1.23 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 239 HIS 0.006 0.001 HIS B 197 PHE 0.028 0.001 PHE B 202 TYR 0.023 0.001 TYR H 81 ARG 0.003 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 638) hydrogen bonds : angle 4.79000 ( 1760) SS BOND : bond 0.00599 ( 1) SS BOND : angle 4.20669 ( 2) covalent geometry : bond 0.00285 (21690) covalent geometry : angle 0.56792 (29970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12928.25 seconds wall clock time: 222 minutes 8.55 seconds (13328.55 seconds total)