Starting phenix.real_space_refine on Wed May 21 01:25:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k29_36835/05_2025/8k29_36835.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k29_36835/05_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_36835/05_2025/8k29_36835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k29_36835/05_2025/8k29_36835.map" model { file = "/net/cci-nas-00/data/ceres_data/8k29_36835/05_2025/8k29_36835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k29_36835/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 12.21, per 1000 atoms: 0.58 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: 5.05 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: 7.68 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: 6.38 Time building geometry restraints manager: 5.87 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.160 Set scattering table: 0.170 Process input model: 49.970 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.190 ------------------------------------------------------------------------------- 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 : 2.041 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: 0.3268 time to fit residues: 216.4805 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 : 2.277 ------------------------------------------------------------------------------- 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 = 0.162702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.120385 restraints weight = 29768.618| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.96 r_work: 0.3229 rms_B_bonded: 2.89 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: 0.8163 moved from start: 0.1756 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 7.921 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 : 12.05 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 6.02679 ( 1760) SS BOND : bond 0.00258 ( 1) SS BOND : angle 2.26446 ( 2) covalent geometry : bond 0.00348 (21690) covalent geometry : angle 0.64265 (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 : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8682 (m-10) cc_final: 0.8389 (m-10) REVERT: A 158 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8070 (mmmt) REVERT: B 26 MET cc_start: 0.9013 (tpt) cc_final: 0.8714 (tpt) REVERT: B 115 ASP cc_start: 0.8711 (m-30) cc_final: 0.8262 (p0) REVERT: B 202 PHE cc_start: 0.8369 (p90) cc_final: 0.8158 (p90) REVERT: B 213 THR cc_start: 0.8930 (t) cc_final: 0.8690 (t) REVERT: B 214 MET cc_start: 0.8842 (mmm) cc_final: 0.8395 (mmm) REVERT: C 191 MET cc_start: 0.8762 (mtm) cc_final: 0.8530 (mtm) REVERT: C 275 ASP cc_start: 0.8225 (m-30) cc_final: 0.7402 (m-30) REVERT: D 5 LYS cc_start: 0.8027 (mppt) cc_final: 0.7659 (mmtm) REVERT: D 217 ASP cc_start: 0.7939 (p0) cc_final: 0.7683 (p0) REVERT: E 204 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7876 (mt-10) REVERT: F 99 TYR cc_start: 0.8904 (t80) cc_final: 0.8640 (t80) REVERT: F 162 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7795 (tp30) REVERT: H 78 LEU cc_start: 0.7444 (tp) cc_final: 0.7136 (tp) outliers start: 68 outliers final: 27 residues processed: 347 average time/residue: 0.2976 time to fit residues: 162.9154 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 : 2.124 ------------------------------------------------------------------------------- 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: 0.7980 chunk 178 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 179 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.159519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115404 restraints weight = 29184.328| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.91 r_work: 0.3155 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 21691 Z= 0.189 Angle : 0.616 8.611 29972 Z= 0.339 Chirality : 0.044 0.248 3474 Planarity : 0.005 0.135 3433 Dihedral : 21.286 178.276 4233 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.04 % Favored : 94.75 % Rotamer: Outliers : 3.57 % Allowed : 25.28 % Favored : 71.15 % 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: -2.12 (0.16), residues: 2379 helix: -1.16 (0.19), residues: 653 sheet: -0.87 (0.24), residues: 450 loop : -1.74 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 239 HIS 0.006 0.001 HIS B 197 PHE 0.016 0.001 PHE B 64 TYR 0.014 0.001 TYR E 190 ARG 0.004 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 638) hydrogen bonds : angle 5.45187 ( 1760) SS BOND : bond 0.00153 ( 1) SS BOND : angle 1.63703 ( 2) covalent geometry : bond 0.00415 (21690) covalent geometry : angle 0.61613 (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 332 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7833 (t0) cc_final: 0.7327 (t0) REVERT: A 137 TYR cc_start: 0.8794 (m-10) cc_final: 0.8469 (m-10) REVERT: B 26 MET cc_start: 0.9153 (tpt) cc_final: 0.8862 (tpt) REVERT: B 62 SER cc_start: 0.8803 (t) cc_final: 0.8500 (p) REVERT: B 115 ASP cc_start: 0.8617 (m-30) cc_final: 0.7812 (t0) REVERT: C 5 LYS cc_start: 0.6202 (tmtt) cc_final: 0.5905 (tmtt) REVERT: C 121 TYR cc_start: 0.8981 (t80) cc_final: 0.8200 (t80) REVERT: D 5 LYS cc_start: 0.8127 (mppt) cc_final: 0.7732 (mmtm) REVERT: E 204 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8265 (mm-30) REVERT: F 9 VAL cc_start: 0.8308 (t) cc_final: 0.8054 (p) REVERT: F 99 TYR cc_start: 0.8937 (t80) cc_final: 0.8619 (t80) REVERT: G 235 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8058 (p) REVERT: G 262 TYR cc_start: 0.8843 (m-80) cc_final: 0.8331 (m-80) REVERT: H 16 ILE cc_start: 0.8273 (tp) cc_final: 0.7925 (pt) REVERT: H 38 MET cc_start: 0.7675 (mmm) cc_final: 0.7128 (mmm) REVERT: H 224 MET cc_start: 0.8287 (tpt) cc_final: 0.7956 (tpp) REVERT: I 135 VAL cc_start: 0.5791 (OUTLIER) cc_final: 0.5346 (t) outliers start: 70 outliers final: 37 residues processed: 311 average time/residue: 0.3160 time to fit residues: 154.1163 Evaluate side-chains 282 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 2.161 ------------------------------------------------------------------------------- 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 D residue 284 THR 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: 8.9990 chunk 34 optimal weight: 0.0980 chunk 239 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 158 ASN E 33 ASN F 33 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.153397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107858 restraints weight = 29210.885| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.89 r_work: 0.3045 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 21691 Z= 0.304 Angle : 0.690 9.744 29972 Z= 0.374 Chirality : 0.047 0.234 3474 Planarity : 0.005 0.139 3433 Dihedral : 21.345 178.724 4225 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer: Outliers : 4.28 % Allowed : 24.52 % Favored : 71.20 % 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: -2.05 (0.16), residues: 2379 helix: -1.00 (0.19), residues: 645 sheet: -0.85 (0.24), residues: 437 loop : -1.73 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 239 HIS 0.007 0.002 HIS F 189 PHE 0.014 0.002 PHE D 271 TYR 0.017 0.002 TYR A 73 ARG 0.006 0.001 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 638) hydrogen bonds : angle 5.49430 ( 1760) SS BOND : bond 0.02046 ( 1) SS BOND : angle 3.83956 ( 2) covalent geometry : bond 0.00685 (21690) covalent geometry : angle 0.68946 (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 327 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 243 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 TYR cc_start: 0.8081 (t80) cc_final: 0.7862 (t80) REVERT: A 137 TYR cc_start: 0.8953 (m-10) cc_final: 0.8607 (m-10) REVERT: A 150 GLN cc_start: 0.9018 (pm20) cc_final: 0.8676 (pm20) REVERT: B 26 MET cc_start: 0.9240 (tpt) cc_final: 0.8767 (tpt) REVERT: B 62 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8450 (p) REVERT: B 115 ASP cc_start: 0.8560 (m-30) cc_final: 0.7849 (t0) REVERT: B 182 MET cc_start: 0.8654 (ttp) cc_final: 0.8211 (ttp) REVERT: C 5 LYS cc_start: 0.6546 (tmtt) cc_final: 0.6173 (tmtt) REVERT: C 121 TYR cc_start: 0.9064 (t80) cc_final: 0.8225 (t80) REVERT: D 5 LYS cc_start: 0.8253 (mppt) cc_final: 0.7860 (mmtm) REVERT: D 104 GLN cc_start: 0.9081 (tt0) cc_final: 0.8876 (tt0) REVERT: E 202 SER cc_start: 0.9213 (p) cc_final: 0.9000 (p) REVERT: E 204 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8335 (mm-30) REVERT: F 9 VAL cc_start: 0.8685 (t) cc_final: 0.8460 (p) REVERT: F 162 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7484 (mp0) REVERT: G 235 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8131 (p) REVERT: G 262 TYR cc_start: 0.9088 (m-80) cc_final: 0.8869 (m-80) REVERT: H 118 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7127 (ttm170) REVERT: H 224 MET cc_start: 0.8401 (tpt) cc_final: 0.8138 (tpp) outliers start: 84 outliers final: 50 residues processed: 303 average time/residue: 0.3088 time to fit residues: 147.5545 Evaluate side-chains 274 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 114 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 184 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 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 151 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 33 ASN 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 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 94 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 86 VAL Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 103 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 235 optimal weight: 0.0030 chunk 187 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 147 optimal weight: 0.0570 chunk 230 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 overall best weight: 0.5510 ------------------------------------------------------------------------------- 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** B 180 GLN D 63 GLN D 72 HIS D 158 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 221 GLN ** H 294 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 = 0.3934 r_free = 0.3934 target = 0.158586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115694 restraints weight = 29219.036| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.78 r_work: 0.3147 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21691 Z= 0.139 Angle : 0.583 10.519 29972 Z= 0.318 Chirality : 0.042 0.308 3474 Planarity : 0.005 0.134 3433 Dihedral : 21.279 179.482 4225 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.13 % Favored : 94.66 % Rotamer: Outliers : 3.21 % Allowed : 25.69 % 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: -1.76 (0.16), residues: 2379 helix: -0.68 (0.19), residues: 644 sheet: -0.60 (0.26), residues: 401 loop : -1.62 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 239 HIS 0.006 0.001 HIS B 197 PHE 0.022 0.001 PHE B 202 TYR 0.013 0.001 TYR H 117 ARG 0.005 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 638) hydrogen bonds : angle 5.12449 ( 1760) SS BOND : bond 0.00150 ( 1) SS BOND : angle 2.56899 ( 2) covalent geometry : bond 0.00303 (21690) covalent geometry : angle 0.58253 (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 322 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 259 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8796 (m-10) cc_final: 0.8430 (m-10) REVERT: B 108 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: B 115 ASP cc_start: 0.8383 (m-30) cc_final: 0.7923 (t0) REVERT: B 182 MET cc_start: 0.8591 (ttp) cc_final: 0.8224 (ttp) REVERT: C 5 LYS cc_start: 0.6571 (tmtt) cc_final: 0.6091 (tmtt) REVERT: C 121 TYR cc_start: 0.8920 (t80) cc_final: 0.8119 (t80) REVERT: C 183 VAL cc_start: 0.8748 (m) cc_final: 0.8486 (p) REVERT: D 5 LYS cc_start: 0.8135 (mppt) cc_final: 0.7893 (mmtm) REVERT: D 104 GLN cc_start: 0.8985 (tt0) cc_final: 0.8714 (tt0) REVERT: D 227 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8502 (pt0) REVERT: E 202 SER cc_start: 0.9036 (p) cc_final: 0.8819 (p) REVERT: F 9 VAL cc_start: 0.8219 (t) cc_final: 0.7975 (p) REVERT: G 139 ILE cc_start: 0.7533 (mm) cc_final: 0.7318 (mm) REVERT: G 235 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8095 (p) REVERT: H 38 MET cc_start: 0.7727 (mmm) cc_final: 0.7100 (mmm) REVERT: H 118 ARG cc_start: 0.7389 (ttm-80) cc_final: 0.7071 (ttm170) outliers start: 63 outliers final: 39 residues processed: 302 average time/residue: 0.3086 time to fit residues: 146.6692 Evaluate side-chains 283 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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 108 ASP Chi-restraints excluded: chain B residue 141 VAL 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 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 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 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 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 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 164 VAL Chi-restraints excluded: chain G residue 235 THR 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: 4.9990 chunk 202 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 201 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** B 84 ASN D 63 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 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 ** 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 17 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 = 0.3903 r_free = 0.3903 target = 0.155985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112508 restraints weight = 29024.334| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.74 r_work: 0.3111 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21691 Z= 0.207 Angle : 0.607 9.255 29972 Z= 0.328 Chirality : 0.044 0.288 3474 Planarity : 0.005 0.133 3433 Dihedral : 21.233 179.393 4225 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.67 % Favored : 94.12 % Rotamer: Outliers : 3.57 % Allowed : 25.99 % 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: -1.64 (0.16), residues: 2379 helix: -0.52 (0.20), residues: 644 sheet: -0.56 (0.26), residues: 401 loop : -1.56 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 239 HIS 0.007 0.001 HIS B 197 PHE 0.022 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 0.03868 ( 638) hydrogen bonds : angle 5.13446 ( 1760) SS BOND : bond 0.00088 ( 1) SS BOND : angle 3.79272 ( 2) covalent geometry : bond 0.00468 (21690) covalent geometry : angle 0.60644 (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 315 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 245 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7988 (t0) cc_final: 0.7758 (t0) REVERT: A 137 TYR cc_start: 0.8829 (m-10) cc_final: 0.8565 (m-10) REVERT: B 26 MET cc_start: 0.9100 (tpt) cc_final: 0.8704 (tpt) REVERT: B 108 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: B 115 ASP cc_start: 0.8355 (m-30) cc_final: 0.7932 (t0) REVERT: B 182 MET cc_start: 0.8552 (ttp) cc_final: 0.8177 (ttp) REVERT: C 5 LYS cc_start: 0.6689 (tmtt) cc_final: 0.6116 (tmtt) REVERT: C 121 TYR cc_start: 0.8932 (t80) cc_final: 0.8165 (t80) REVERT: C 183 VAL cc_start: 0.8899 (m) cc_final: 0.8633 (p) REVERT: D 5 LYS cc_start: 0.8170 (mppt) cc_final: 0.7917 (mmtm) REVERT: D 104 GLN cc_start: 0.9021 (tt0) cc_final: 0.8740 (tt0) REVERT: D 131 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8245 (ttt90) REVERT: D 227 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: E 202 SER cc_start: 0.9090 (p) cc_final: 0.8877 (p) REVERT: F 9 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8091 (p) REVERT: G 235 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8172 (p) REVERT: H 38 MET cc_start: 0.7803 (mmm) cc_final: 0.7175 (mmm) REVERT: H 78 LEU cc_start: 0.7698 (tp) cc_final: 0.7484 (tt) REVERT: H 118 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7309 (ttm-80) REVERT: H 169 ILE cc_start: 0.7019 (tt) cc_final: 0.6767 (tp) outliers start: 70 outliers final: 53 residues processed: 295 average time/residue: 0.3188 time to fit residues: 148.4621 Evaluate side-chains 292 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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 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 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 131 ARG 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 33 ASN 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 224 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 33 ASN 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 22 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN 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 100 SER 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 69 LEU 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: 0.8980 chunk 200 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 235 optimal weight: 40.0000 chunk 65 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 84 ASN B 222 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** G 294 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112386 restraints weight = 29054.364| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.81 r_work: 0.3102 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3302 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= 0.207 Angle : 0.607 9.304 29972 Z= 0.327 Chirality : 0.043 0.255 3474 Planarity : 0.005 0.133 3433 Dihedral : 21.238 179.751 4225 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.76 % Favored : 94.07 % Rotamer: Outliers : 3.62 % Allowed : 26.20 % Favored : 70.18 % 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: -1.58 (0.17), residues: 2379 helix: -0.45 (0.20), residues: 645 sheet: -0.62 (0.26), residues: 394 loop : -1.49 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 239 HIS 0.007 0.001 HIS B 197 PHE 0.025 0.001 PHE B 202 TYR 0.015 0.001 TYR H 117 ARG 0.011 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 638) hydrogen bonds : angle 5.12261 ( 1760) SS BOND : bond 0.00329 ( 1) SS BOND : angle 3.12700 ( 2) covalent geometry : bond 0.00465 (21690) covalent geometry : angle 0.60665 (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 313 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 242 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7952 (tpp) cc_final: 0.7732 (tpp) REVERT: A 137 TYR cc_start: 0.8858 (m-10) cc_final: 0.8583 (m-10) REVERT: B 26 MET cc_start: 0.9137 (tpt) cc_final: 0.8758 (tpt) REVERT: B 108 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8185 (m-30) REVERT: B 115 ASP cc_start: 0.8330 (m-30) cc_final: 0.7934 (t0) REVERT: B 182 MET cc_start: 0.8625 (ttp) cc_final: 0.8211 (ttp) REVERT: C 121 TYR cc_start: 0.8912 (t80) cc_final: 0.8138 (t80) REVERT: C 183 VAL cc_start: 0.8947 (m) cc_final: 0.8686 (p) REVERT: D 5 LYS cc_start: 0.8157 (mppt) cc_final: 0.7910 (mmtm) REVERT: D 38 MET cc_start: 0.8824 (mmt) cc_final: 0.8495 (mmp) REVERT: D 104 GLN cc_start: 0.9062 (tt0) cc_final: 0.8758 (tt0) REVERT: D 131 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8284 (ttt90) REVERT: D 227 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: E 117 TYR cc_start: 0.8880 (t80) cc_final: 0.8672 (t80) REVERT: E 202 SER cc_start: 0.9086 (p) cc_final: 0.8883 (p) REVERT: F 9 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8118 (p) REVERT: F 162 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7682 (mp0) REVERT: G 235 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8184 (p) REVERT: H 38 MET cc_start: 0.7789 (mmm) cc_final: 0.7167 (mmm) REVERT: H 78 LEU cc_start: 0.7721 (tp) cc_final: 0.7504 (tt) REVERT: H 118 ARG cc_start: 0.7476 (ttm-80) cc_final: 0.7235 (ttm-80) REVERT: H 169 ILE cc_start: 0.7069 (tt) cc_final: 0.6790 (tp) outliers start: 71 outliers final: 59 residues processed: 290 average time/residue: 0.3012 time to fit residues: 138.0382 Evaluate side-chains 303 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 2.286 ------------------------------------------------------------------------------- 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 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 101 CYS 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 88 ASP 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 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 131 ARG Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 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 33 ASN 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 224 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 164 VAL 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 132 ASN 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 34 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 266 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 119 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 52 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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** B 16 ASN C 146 ASN D 63 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 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 ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.156141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112504 restraints weight = 29157.086| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.84 r_work: 0.3110 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21691 Z= 0.179 Angle : 0.595 9.444 29972 Z= 0.321 Chirality : 0.043 0.235 3474 Planarity : 0.005 0.133 3433 Dihedral : 21.233 179.926 4225 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 3.98 % Allowed : 26.15 % Favored : 69.88 % 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: -1.51 (0.17), residues: 2379 helix: -0.39 (0.20), residues: 647 sheet: -0.61 (0.26), residues: 394 loop : -1.44 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 239 HIS 0.006 0.001 HIS B 197 PHE 0.026 0.001 PHE B 202 TYR 0.015 0.001 TYR H 117 ARG 0.011 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 638) hydrogen bonds : angle 5.06124 ( 1760) SS BOND : bond 0.00184 ( 1) SS BOND : angle 2.76484 ( 2) covalent geometry : bond 0.00399 (21690) covalent geometry : angle 0.59495 (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 324 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 246 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7953 (tpp) cc_final: 0.7751 (tpp) REVERT: A 97 ASP cc_start: 0.7902 (t0) cc_final: 0.7580 (t0) REVERT: A 137 TYR cc_start: 0.8862 (m-10) cc_final: 0.8547 (m-10) REVERT: B 26 MET cc_start: 0.9110 (tpt) cc_final: 0.8737 (tpt) REVERT: B 108 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: B 115 ASP cc_start: 0.8312 (m-30) cc_final: 0.7922 (t0) REVERT: B 182 MET cc_start: 0.8631 (ttp) cc_final: 0.8201 (ttp) REVERT: C 121 TYR cc_start: 0.8896 (t80) cc_final: 0.8125 (t80) REVERT: C 168 GLU cc_start: 0.8489 (tt0) cc_final: 0.8288 (tt0) REVERT: C 183 VAL cc_start: 0.8865 (m) cc_final: 0.8600 (p) REVERT: D 5 LYS cc_start: 0.8145 (mppt) cc_final: 0.7907 (mmtm) REVERT: D 38 MET cc_start: 0.8759 (mmt) cc_final: 0.8411 (mmp) REVERT: D 104 GLN cc_start: 0.9052 (tt0) cc_final: 0.8761 (tt0) REVERT: D 131 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8231 (ttt90) REVERT: D 137 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: D 185 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8534 (mt) REVERT: D 227 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: E 202 SER cc_start: 0.9076 (p) cc_final: 0.8866 (p) REVERT: F 9 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8073 (p) REVERT: F 162 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7672 (mp0) REVERT: G 156 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8303 (mm) REVERT: G 235 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8195 (p) REVERT: H 38 MET cc_start: 0.7777 (mmm) cc_final: 0.7156 (mmm) REVERT: H 78 LEU cc_start: 0.7730 (tp) cc_final: 0.7495 (tt) REVERT: H 119 TYR cc_start: 0.7942 (m-10) cc_final: 0.7656 (m-10) REVERT: H 169 ILE cc_start: 0.7051 (tt) cc_final: 0.6774 (tp) outliers start: 78 outliers final: 60 residues processed: 298 average time/residue: 0.3022 time to fit residues: 142.3806 Evaluate side-chains 307 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 101 CYS 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 88 ASP 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 131 ARG Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 LEU 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 33 ASN 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 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 164 VAL 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 22 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 132 ASN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 215 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 172 optimal weight: 0.3980 chunk 224 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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** B 16 ASN C 146 ASN D 63 GLN ** D 227 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112679 restraints weight = 29065.603| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.74 r_work: 0.3120 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21691 Z= 0.187 Angle : 0.606 9.565 29972 Z= 0.326 Chirality : 0.043 0.224 3474 Planarity : 0.005 0.133 3433 Dihedral : 21.225 179.716 4225 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 3.82 % Allowed : 26.25 % Favored : 69.93 % 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: -1.49 (0.17), residues: 2379 helix: -0.37 (0.20), residues: 647 sheet: -0.58 (0.27), residues: 388 loop : -1.43 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP H 239 HIS 0.006 0.001 HIS B 197 PHE 0.027 0.001 PHE B 202 TYR 0.024 0.001 TYR H 81 ARG 0.011 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 638) hydrogen bonds : angle 5.06327 ( 1760) SS BOND : bond 0.01377 ( 1) SS BOND : angle 5.00464 ( 2) covalent geometry : bond 0.00420 (21690) covalent geometry : angle 0.60428 (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 316 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 241 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7932 (tpp) cc_final: 0.7724 (tpp) REVERT: A 97 ASP cc_start: 0.7874 (t0) cc_final: 0.7561 (t0) REVERT: A 137 TYR cc_start: 0.8800 (m-10) cc_final: 0.8426 (m-10) REVERT: B 26 MET cc_start: 0.9125 (tpt) cc_final: 0.8714 (tpt) REVERT: B 108 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8252 (m-30) REVERT: B 115 ASP cc_start: 0.8301 (m-30) cc_final: 0.7937 (t0) REVERT: B 182 MET cc_start: 0.8717 (ttp) cc_final: 0.8253 (ttp) REVERT: C 121 TYR cc_start: 0.8914 (t80) cc_final: 0.8130 (t80) REVERT: C 183 VAL cc_start: 0.8844 (m) cc_final: 0.8554 (p) REVERT: D 5 LYS cc_start: 0.8150 (mppt) cc_final: 0.7906 (mmtm) REVERT: D 38 MET cc_start: 0.8761 (mmt) cc_final: 0.8398 (mmp) REVERT: D 131 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8262 (ttt90) REVERT: D 137 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: D 185 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8552 (mt) REVERT: D 227 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: E 117 TYR cc_start: 0.8852 (t80) cc_final: 0.8614 (t80) REVERT: E 202 SER cc_start: 0.9082 (p) cc_final: 0.8865 (p) REVERT: F 9 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8079 (p) REVERT: F 162 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7636 (mp0) REVERT: G 235 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8176 (p) REVERT: H 38 MET cc_start: 0.7760 (mmm) cc_final: 0.7133 (mmm) REVERT: H 78 LEU cc_start: 0.7698 (tp) cc_final: 0.7474 (tt) REVERT: H 119 TYR cc_start: 0.7781 (m-10) cc_final: 0.7555 (m-10) REVERT: H 169 ILE cc_start: 0.6871 (tt) cc_final: 0.6566 (tp) REVERT: H 263 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7252 (mtt-85) outliers start: 75 outliers final: 59 residues processed: 291 average time/residue: 0.2930 time to fit residues: 134.9730 Evaluate side-chains 303 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 237 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 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 29 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 88 ASP 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 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 131 ARG Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 LEU 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 33 ASN 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 224 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 164 VAL 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 22 LEU 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 284 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 62 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 36 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN D 63 GLN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN G 221 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115269 restraints weight = 29199.036| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.72 r_work: 0.3157 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21691 Z= 0.140 Angle : 0.585 9.661 29972 Z= 0.315 Chirality : 0.042 0.222 3474 Planarity : 0.005 0.132 3433 Dihedral : 21.214 179.296 4225 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.25 % Favored : 94.58 % Rotamer: Outliers : 3.26 % Allowed : 26.96 % Favored : 69.78 % 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: -1.41 (0.17), residues: 2379 helix: -0.26 (0.20), residues: 646 sheet: -0.63 (0.26), residues: 398 loop : -1.38 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP H 239 HIS 0.005 0.001 HIS B 197 PHE 0.028 0.001 PHE B 202 TYR 0.025 0.001 TYR H 81 ARG 0.010 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 638) hydrogen bonds : angle 4.96126 ( 1760) SS BOND : bond 0.00719 ( 1) SS BOND : angle 4.50723 ( 2) covalent geometry : bond 0.00310 (21690) covalent geometry : angle 0.58339 (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 313 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 249 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7940 (tpp) cc_final: 0.7739 (tpp) REVERT: A 97 ASP cc_start: 0.7834 (t0) cc_final: 0.7606 (t0) REVERT: A 137 TYR cc_start: 0.8738 (m-10) cc_final: 0.8346 (m-10) REVERT: B 16 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8335 (p0) REVERT: B 26 MET cc_start: 0.9067 (tpt) cc_final: 0.8698 (tpt) REVERT: B 108 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: B 115 ASP cc_start: 0.8334 (m-30) cc_final: 0.7988 (t0) REVERT: B 182 MET cc_start: 0.8678 (ttp) cc_final: 0.8249 (ttp) REVERT: C 5 LYS cc_start: 0.6313 (tmtt) cc_final: 0.5836 (tmtt) REVERT: C 121 TYR cc_start: 0.8880 (t80) cc_final: 0.8112 (t80) REVERT: C 183 VAL cc_start: 0.8755 (m) cc_final: 0.8477 (p) REVERT: D 5 LYS cc_start: 0.8116 (mppt) cc_final: 0.7892 (mmtm) REVERT: D 185 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8497 (mt) REVERT: D 227 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: E 117 TYR cc_start: 0.8717 (t80) cc_final: 0.8455 (t80) REVERT: E 171 ASP cc_start: 0.7732 (m-30) cc_final: 0.7304 (p0) REVERT: E 202 SER cc_start: 0.9020 (p) cc_final: 0.8793 (p) REVERT: F 9 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (p) REVERT: F 162 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7649 (mp0) REVERT: F 300 VAL cc_start: 0.9047 (m) cc_final: 0.8831 (m) REVERT: G 139 ILE cc_start: 0.7627 (mm) cc_final: 0.7424 (mm) REVERT: G 235 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8138 (p) REVERT: G 262 TYR cc_start: 0.8909 (m-80) cc_final: 0.8637 (m-80) REVERT: H 38 MET cc_start: 0.7724 (mmm) cc_final: 0.7092 (mmm) REVERT: H 78 LEU cc_start: 0.7690 (tp) cc_final: 0.7463 (tt) REVERT: H 98 GLU cc_start: 0.8311 (pm20) cc_final: 0.7639 (pt0) REVERT: H 119 TYR cc_start: 0.7747 (m-10) cc_final: 0.7450 (m-10) REVERT: H 169 ILE cc_start: 0.6755 (tt) cc_final: 0.6337 (tp) outliers start: 64 outliers final: 55 residues processed: 293 average time/residue: 0.3045 time to fit residues: 142.2910 Evaluate side-chains 302 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 241 time to evaluate : 2.105 ------------------------------------------------------------------------------- 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 141 VAL 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 88 ASP 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 157 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 185 LEU 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 33 ASN 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 224 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 33 ASN 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 164 VAL 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 132 ASN Chi-restraints excluded: chain G residue 164 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 34 THR Chi-restraints excluded: chain H residue 62 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 44 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 69 optimal weight: 0.0770 chunk 211 optimal weight: 9.9990 chunk 37 optimal weight: 0.2980 chunk 236 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 146 ASN D 63 GLN ** D 227 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116848 restraints weight = 29255.522| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.77 r_work: 0.3183 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21691 Z= 0.133 Angle : 0.577 9.770 29972 Z= 0.311 Chirality : 0.042 0.220 3474 Planarity : 0.005 0.131 3433 Dihedral : 21.186 179.066 4225 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 3.36 % Allowed : 27.22 % Favored : 69.42 % 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: -1.32 (0.17), residues: 2379 helix: -0.21 (0.20), residues: 644 sheet: -0.73 (0.25), residues: 428 loop : -1.25 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP H 239 HIS 0.003 0.001 HIS B 197 PHE 0.029 0.001 PHE B 202 TYR 0.025 0.001 TYR H 81 ARG 0.011 0.000 ARG G 133 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 638) hydrogen bonds : angle 4.88298 ( 1760) SS BOND : bond 0.00589 ( 1) SS BOND : angle 4.23441 ( 2) covalent geometry : bond 0.00294 (21690) covalent geometry : angle 0.57614 (29970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12611.66 seconds wall clock time: 218 minutes 36.42 seconds (13116.42 seconds total)