Starting phenix.real_space_refine on Sun Jul 5 11:14:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zzr_75014/07_2026/9zzr_75014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zzr_75014/07_2026/9zzr_75014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zzr_75014/07_2026/9zzr_75014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zzr_75014/07_2026/9zzr_75014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zzr_75014/07_2026/9zzr_75014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zzr_75014/07_2026/9zzr_75014.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 56 5.49 5 S 145 5.16 5 C 16648 2.51 5 N 4689 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26730 Number of models: 1 Model: "" Number of chains: 22 Chain: "R" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2379 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Chain: "V" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2379 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Chain: "W" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "O" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "E" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "K" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "J" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 460 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "X" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1912 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 5, 'TRANS': 230} Chain breaks: 3 Chain: "D" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2288 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 7, 'TRANS': 295} Chain breaks: 2 Chain: "C" Number of atoms: 2551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2551 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 11, 'TRANS': 312} Chain breaks: 1 Chain: "B" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2523 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 2 Chain: "F" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2397 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 8, 'TRANS': 305} Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ANP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.64, per 1000 atoms: 0.21 Number of scatterers: 26730 At special positions: 0 Unit cell: (124.147, 132.479, 239.128, 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 145 16.00 P 56 15.00 O 5192 8.00 N 4689 7.00 C 16648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 926.1 milliseconds 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6200 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 16 sheets defined 51.7% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 34 through 44 removed outlier: 3.588A pdb=" N GLU R 43 " --> pdb=" O LYS R 39 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 55 Processing helix chain 'R' and resid 56 through 63 removed outlier: 3.930A pdb=" N ILE R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 82 Processing helix chain 'R' and resid 89 through 97 Processing helix chain 'R' and resid 106 through 114 Processing helix chain 'R' and resid 132 through 144 Processing helix chain 'R' and resid 145 through 146 No H-bonds generated for 'chain 'R' and resid 145 through 146' Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 167 through 178 removed outlier: 3.642A pdb=" N LEU R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 188 removed outlier: 3.664A pdb=" N ASN R 188 " --> pdb=" O ASP R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 211 removed outlier: 3.945A pdb=" N THR R 201 " --> pdb=" O THR R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 232 removed outlier: 3.841A pdb=" N ARG R 229 " --> pdb=" O THR R 225 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 260 Processing helix chain 'R' and resid 289 through 294 Processing helix chain 'V' and resid 24 through 29 Processing helix chain 'V' and resid 34 through 42 Processing helix chain 'V' and resid 48 through 54 Processing helix chain 'V' and resid 56 through 63 removed outlier: 3.581A pdb=" N ILE V 63 " --> pdb=" O GLU V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 82 Processing helix chain 'V' and resid 89 through 97 Processing helix chain 'V' and resid 106 through 114 Processing helix chain 'V' and resid 132 through 144 removed outlier: 3.572A pdb=" N ILE V 136 " --> pdb=" O GLY V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 145 through 146 No H-bonds generated for 'chain 'V' and resid 145 through 146' Processing helix chain 'V' and resid 147 through 151 Processing helix chain 'V' and resid 167 through 179 removed outlier: 3.677A pdb=" N LEU V 171 " --> pdb=" O ARG V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 181 through 188 removed outlier: 3.574A pdb=" N VAL V 185 " --> pdb=" O SER V 181 " (cutoff:3.500A) Processing helix chain 'V' and resid 196 through 212 removed outlier: 4.158A pdb=" N VAL V 212 " --> pdb=" O SER V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 232 removed outlier: 4.041A pdb=" N THR V 230 " --> pdb=" O ALA V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 260 Processing helix chain 'V' and resid 288 through 296 removed outlier: 4.080A pdb=" N ILE V 292 " --> pdb=" O GLY V 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 31 Processing helix chain 'W' and resid 34 through 45 Processing helix chain 'W' and resid 48 through 54 Processing helix chain 'W' and resid 56 through 62 Processing helix chain 'W' and resid 67 through 82 Processing helix chain 'W' and resid 88 through 98 removed outlier: 3.561A pdb=" N PHE W 92 " --> pdb=" O THR W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 114 Processing helix chain 'W' and resid 132 through 144 removed outlier: 3.722A pdb=" N CYS W 137 " --> pdb=" O LYS W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 151 Processing helix chain 'W' and resid 167 through 179 removed outlier: 3.891A pdb=" N LEU W 171 " --> pdb=" O ARG W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 182 through 187 Processing helix chain 'W' and resid 196 through 214 removed outlier: 3.995A pdb=" N THR W 201 " --> pdb=" O THR W 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN W 202 " --> pdb=" O ASP W 198 " (cutoff:3.500A) Processing helix chain 'W' and resid 225 through 232 removed outlier: 3.527A pdb=" N ARG W 229 " --> pdb=" O THR W 225 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR W 230 " --> pdb=" O ALA W 226 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR W 232 " --> pdb=" O TYR W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 260 Processing helix chain 'W' and resid 288 through 296 removed outlier: 4.030A pdb=" N ILE W 292 " --> pdb=" O GLY W 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 32 removed outlier: 3.526A pdb=" N GLN O 30 " --> pdb=" O ARG O 27 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY O 32 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 45 Processing helix chain 'O' and resid 48 through 54 Processing helix chain 'O' and resid 56 through 63 removed outlier: 3.755A pdb=" N ILE O 63 " --> pdb=" O GLU O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 82 removed outlier: 3.759A pdb=" N ALA O 71 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP O 72 " --> pdb=" O GLU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 98 removed outlier: 3.945A pdb=" N PHE O 92 " --> pdb=" O THR O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 134 through 144 Processing helix chain 'O' and resid 145 through 146 No H-bonds generated for 'chain 'O' and resid 145 through 146' Processing helix chain 'O' and resid 147 through 151 Processing helix chain 'O' and resid 167 through 179 removed outlier: 3.938A pdb=" N LEU O 171 " --> pdb=" O ARG O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 185 Processing helix chain 'O' and resid 196 through 214 removed outlier: 3.504A pdb=" N GLN O 200 " --> pdb=" O ASN O 196 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR O 201 " --> pdb=" O THR O 197 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN O 202 " --> pdb=" O ASP O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 232 removed outlier: 4.057A pdb=" N THR O 230 " --> pdb=" O ALA O 226 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR O 232 " --> pdb=" O TYR O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 288 through 296 removed outlier: 3.767A pdb=" N ILE O 292 " --> pdb=" O GLY O 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 31 removed outlier: 3.502A pdb=" N GLN E 30 " --> pdb=" O ARG E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 45 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 88 through 98 removed outlier: 3.873A pdb=" N PHE E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.762A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 179 removed outlier: 3.938A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.861A pdb=" N THR E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 232 removed outlier: 3.573A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 288 through 296 removed outlier: 4.012A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 31 removed outlier: 3.651A pdb=" N LEU K 28 " --> pdb=" O ILE K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 63 removed outlier: 3.520A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 Processing helix chain 'K' and resid 89 through 98 Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 134 through 144 Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 179 removed outlier: 3.956A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 214 removed outlier: 3.963A pdb=" N THR K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN K 202 " --> pdb=" O ASP K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 232 removed outlier: 4.027A pdb=" N THR K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR K 232 " --> pdb=" O TYR K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.882A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 28 removed outlier: 3.683A pdb=" N GLU X 28 " --> pdb=" O LEU X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 88 through 100 Processing helix chain 'X' and resid 104 through 113 Processing helix chain 'X' and resid 122 through 140 removed outlier: 4.148A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 163 Processing helix chain 'X' and resid 165 through 188 removed outlier: 5.100A pdb=" N THR X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU X 173 " --> pdb=" O GLN X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 233 Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.651A pdb=" N HIS D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 62 Processing helix chain 'D' and resid 68 through 79 removed outlier: 3.668A pdb=" N THR D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 142 through 154 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 174 through 192 Processing helix chain 'D' and resid 207 through 213 removed outlier: 4.098A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 240 Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.739A pdb=" N TRP D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 269' Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.783A pdb=" N LEU C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 130 through 143 removed outlier: 4.005A pdb=" N GLN C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 187 removed outlier: 3.672A pdb=" N HIS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 removed outlier: 3.926A pdb=" N ALA C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 244 through 250 removed outlier: 3.950A pdb=" N PHE C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 277 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.755A pdb=" N LEU B 6 " --> pdb=" O ASP B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 42 through 58 removed outlier: 3.601A pdb=" N LEU B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 71 removed outlier: 3.590A pdb=" N LEU B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.820A pdb=" N HIS B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 125 through 126 No H-bonds generated for 'chain 'B' and resid 125 through 126' Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.587A pdb=" N LEU B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 186 through 204 removed outlier: 4.750A pdb=" N VAL B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Proline residue: B 199 - end of helix Processing helix chain 'B' and resid 215 through 223 removed outlier: 3.955A pdb=" N PHE B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 250 removed outlier: 4.711A pdb=" N ARG B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.872A pdb=" N GLN B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 removed outlier: 4.335A pdb=" N GLU F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 30' Processing helix chain 'F' and resid 36 through 43 removed outlier: 3.861A pdb=" N LYS F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 56 through 63 Processing helix chain 'F' and resid 67 through 78 Processing helix chain 'F' and resid 79 through 81 No H-bonds generated for 'chain 'F' and resid 79 through 81' Processing helix chain 'F' and resid 89 through 96 removed outlier: 3.516A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 99 No H-bonds generated for 'chain 'F' and resid 97 through 99' Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.677A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 179 removed outlier: 3.775A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 188 Processing helix chain 'F' and resid 196 through 214 removed outlier: 3.662A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 232 removed outlier: 4.077A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 260 removed outlier: 4.492A pdb=" N ALA F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing sheet with id=AA1, first strand: chain 'R' and resid 87 through 88 removed outlier: 3.520A pdb=" N ASN F 267 " --> pdb=" O MET F 125 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY F 127 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 333 through 335 removed outlier: 3.669A pdb=" N ALA R 328 " --> pdb=" O GLY R 335 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE R 122 " --> pdb=" O THR R 298 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU R 300 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU R 124 " --> pdb=" O LEU R 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU R 302 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE R 126 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LYS R 304 " --> pdb=" O PHE R 126 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY R 127 " --> pdb=" O ASN R 267 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLN R 268 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS R 156 " --> pdb=" O TYR R 216 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU R 218 " --> pdb=" O LYS R 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 190 through 193 removed outlier: 5.948A pdb=" N LYS V 156 " --> pdb=" O TYR V 216 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU V 218 " --> pdb=" O LYS V 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'W' and resid 190 through 193 removed outlier: 3.552A pdb=" N ALA W 190 " --> pdb=" O ALA W 157 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS W 156 " --> pdb=" O ALA W 217 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU W 219 " --> pdb=" O LYS W 156 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N MET W 158 " --> pdb=" O LEU W 219 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL W 221 " --> pdb=" O MET W 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE W 160 " --> pdb=" O VAL W 221 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR W 123 " --> pdb=" O ILE W 265 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN W 267 " --> pdb=" O THR W 123 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N MET W 125 " --> pdb=" O ASN W 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY W 333 " --> pdb=" O ASN W 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 333 through 335 removed outlier: 3.513A pdb=" N GLY O 333 " --> pdb=" O ASN O 330 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE O 311 " --> pdb=" O ARG O 303 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE O 122 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU O 300 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU O 124 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU O 302 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE O 126 " --> pdb=" O LEU O 302 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LYS O 304 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR O 123 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASN O 267 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N MET O 125 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU O 219 " --> pdb=" O VAL O 264 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N THR O 266 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL O 221 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET O 158 " --> pdb=" O ILE O 220 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP O 222 " --> pdb=" O MET O 158 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE O 160 " --> pdb=" O ASP O 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 190 through 193 removed outlier: 3.936A pdb=" N ALA E 190 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS E 156 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU E 219 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET E 158 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL E 221 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE E 160 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 333 " --> pdb=" O ASN E 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 190 through 193 removed outlier: 3.611A pdb=" N ALA K 190 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LYS K 156 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU K 219 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET K 158 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL K 221 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE K 160 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR K 123 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN K 267 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N MET K 125 " --> pdb=" O ASN K 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 276 through 279 removed outlier: 6.986A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASP X 42 " --> pdb=" O LEU X 191 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA X 193 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU X 44 " --> pdb=" O ALA X 193 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N THR X 195 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE X 46 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU X 77 " --> pdb=" O LEU X 145 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE X 147 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU X 79 " --> pdb=" O ILE X 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 260 through 262 removed outlier: 6.050A pdb=" N THR D 103 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN D 249 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE D 105 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 251 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY D 107 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N ARG D 253 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU D 277 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU D 295 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASP D 279 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ALA D 293 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 260 through 262 removed outlier: 6.602A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N HIS D 250 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASN D 131 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 203 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D 133 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL D 205 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL D 135 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.237A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 279 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C 283 " --> pdb=" O VAL C 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.237A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 279 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C 283 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 125 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET C 286 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR C 120 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 313 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU C 122 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE C 315 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N CYS C 124 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N TRP C 317 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.823A pdb=" N ARG B 313 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG B 295 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 102 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 296 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLU B 104 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA B 298 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 106 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR B 103 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B 257 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 105 " --> pdb=" O ASN B 257 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU B 254 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL B 210 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE B 256 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 212 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY B 136 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL B 211 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 138 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP B 213 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 140 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR F 87 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AB7, first strand: chain 'F' and resid 328 through 329 1283 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4853 1.32 - 1.45: 6461 1.45 - 1.57: 15535 1.57 - 1.69: 102 1.69 - 1.81: 231 Bond restraints: 27182 Sorted by residual: bond pdb=" N3B ANP W 401 " pdb=" PG ANP W 401 " ideal model delta sigma weight residual 1.795 1.593 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" N3B ANP V 401 " pdb=" PG ANP V 401 " ideal model delta sigma weight residual 1.795 1.596 0.199 2.00e-02 2.50e+03 9.88e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.549 0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" O3A ANP K 401 " pdb=" PB ANP K 401 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.31e+01 ... (remaining 27177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 36555 3.60 - 7.21: 232 7.21 - 10.81: 48 10.81 - 14.41: 7 14.41 - 18.02: 9 Bond angle restraints: 36851 Sorted by residual: angle pdb=" PB ANP K 401 " pdb=" N3B ANP K 401 " pdb=" PG ANP K 401 " ideal model delta sigma weight residual 126.95 108.93 18.02 3.00e+00 1.11e-01 3.61e+01 angle pdb=" PB ANP R 401 " pdb=" N3B ANP R 401 " pdb=" PG ANP R 401 " ideal model delta sigma weight residual 126.95 109.26 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 109.69 17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 109.72 17.23 3.00e+00 1.11e-01 3.30e+01 angle pdb=" PB ANP B 401 " pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 126.95 109.97 16.98 3.00e+00 1.11e-01 3.21e+01 ... (remaining 36846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 15745 34.08 - 68.16: 795 68.16 - 102.24: 77 102.24 - 136.31: 3 136.31 - 170.39: 4 Dihedral angle restraints: 16624 sinusoidal: 6992 harmonic: 9632 Sorted by residual: dihedral pdb=" CD ARG D 300 " pdb=" NE ARG D 300 " pdb=" CZ ARG D 300 " pdb=" NH1 ARG D 300 " ideal model delta sinusoidal sigma weight residual 0.00 46.56 -46.56 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA GLN C 285 " pdb=" C GLN C 285 " pdb=" N MET C 286 " pdb=" CA MET C 286 " ideal model delta harmonic sigma weight residual 180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ALA O 337 " pdb=" C ALA O 337 " pdb=" N LYS O 338 " pdb=" CA LYS O 338 " ideal model delta harmonic sigma weight residual 0.00 24.61 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 16621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4159 0.109 - 0.218: 74 0.218 - 0.326: 12 0.326 - 0.435: 0 0.435 - 0.544: 1 Chirality restraints: 4246 Sorted by residual: chirality pdb=" CG LEU C 297 " pdb=" CB LEU C 297 " pdb=" CD1 LEU C 297 " pdb=" CD2 LEU C 297 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" C3' ANP K 401 " pdb=" C2' ANP K 401 " pdb=" C4' ANP K 401 " pdb=" O3' ANP K 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' ANP E 402 " pdb=" C2' ANP E 402 " pdb=" C4' ANP E 402 " pdb=" O3' ANP E 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 4243 not shown) Planarity restraints: 4620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 300 " 0.789 9.50e-02 1.11e+02 3.54e-01 7.61e+01 pdb=" NE ARG D 300 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG D 300 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 300 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 300 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 235 " 0.284 9.50e-02 1.11e+02 1.27e-01 9.93e+00 pdb=" NE ARG R 235 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG R 235 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG R 235 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 235 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 82 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO F 83 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " -0.037 5.00e-02 4.00e+02 ... (remaining 4617 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 323 2.60 - 3.17: 22702 3.17 - 3.75: 43464 3.75 - 4.32: 60322 4.32 - 4.90: 99662 Nonbonded interactions: 226473 Sorted by model distance: nonbonded pdb=" O GLY R 153 " pdb=" NH1 ARG R 215 " model vdw 2.022 3.120 nonbonded pdb=" O ASP R 222 " pdb=" OG1 THR R 266 " model vdw 2.069 3.040 nonbonded pdb=" OP2 DT J 8 " pdb=" OG1 THR C 288 " model vdw 2.150 3.040 nonbonded pdb=" O LEU D 75 " pdb=" OG1 THR D 79 " model vdw 2.184 3.040 nonbonded pdb=" O1B ANP D 401 " pdb=" O2G ANP D 401 " model vdw 2.202 3.040 ... (remaining 226468 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 'E' and resid 24 through 336) selection = (chain 'F' and (resid 24 through 275 or resid 283 through 336)) selection = (chain 'K' and resid 24 through 336) selection = (chain 'O' and resid 24 through 336) selection = (chain 'R' and (resid 24 through 275 or resid 283 through 336)) selection = (chain 'V' and (resid 24 through 275 or resid 283 through 336)) selection = (chain 'W' and resid 24 through 336) } 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: 8.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 22.720 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 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 : 0.006 0.202 27184 Z= 0.316 Angle : 0.806 18.017 36851 Z= 0.411 Chirality : 0.044 0.544 4246 Planarity : 0.006 0.354 4620 Dihedral : 18.839 170.393 10424 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.65 % Favored : 96.02 % Rotamer: Outliers : 2.83 % Allowed : 23.07 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3317 helix: 0.72 (0.14), residues: 1419 sheet: -0.10 (0.24), residues: 530 loop : -1.22 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 292 TYR 0.029 0.001 TYR C 210 PHE 0.016 0.001 PHE R 126 TRP 0.018 0.002 TRP D 314 HIS 0.014 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.32 (27182) covalent geometry : angle 0.80570 / 0.41 (36851) hydrogen bonds : bond 0.20295 / 14.02 ( 1269) hydrogen bonds : angle 7.60314 / 5.25 ( 3663) Misc. bond : bond 0.00657 / 0.44 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 59 residues processed: 208 average time/residue: 0.5465 time to fit residues: 135.5160 Evaluate side-chains 189 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 130 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 296 SER Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 87 THR Chi-restraints excluded: chain V residue 135 GLN Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 319 CYS Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 330 ASN Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain K residue 319 CYS Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 123 SER Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 319 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** F 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066298 restraints weight = 70039.528| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.43 r_work: 0.2902 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27184 Z= 0.153 Angle : 0.593 14.515 36851 Z= 0.306 Chirality : 0.041 0.169 4246 Planarity : 0.004 0.061 4620 Dihedral : 14.523 173.708 4311 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.83 % Favored : 95.90 % Rotamer: Outliers : 3.69 % Allowed : 21.37 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3317 helix: 0.89 (0.14), residues: 1487 sheet: -0.32 (0.22), residues: 569 loop : -1.26 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 130 TYR 0.019 0.001 TYR W 315 PHE 0.012 0.001 PHE E 129 TRP 0.011 0.002 TRP D 314 HIS 0.013 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (27182) covalent geometry : angle 0.59276 / 0.31 (36851) hydrogen bonds : bond 0.04218 / 2.88 ( 1269) hydrogen bonds : angle 5.61489 / 3.91 ( 3663) Misc. bond : bond 0.00236 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 140 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 62 ASN cc_start: 0.9019 (t0) cc_final: 0.8815 (t0) REVERT: O 189 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8423 (p) REVERT: X 196 GLN cc_start: 0.8007 (mp10) cc_final: 0.7379 (mm-40) REVERT: C 158 ILE cc_start: 0.8972 (mt) cc_final: 0.8592 (tt) REVERT: C 286 MET cc_start: 0.7980 (tpp) cc_final: 0.7699 (tpp) REVERT: B 105 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9181 (tt) REVERT: B 192 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.9039 (pp20) REVERT: B 197 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8219 (mmtp) REVERT: F 223 SER cc_start: 0.8656 (t) cc_final: 0.8413 (p) REVERT: F 243 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8677 (tpt) outliers start: 102 outliers final: 35 residues processed: 225 average time/residue: 0.4980 time to fit residues: 134.1684 Evaluate side-chains 171 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 319 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 30 GLN ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 285 GLN B 115 GLN B 125 GLN B 178 GLN ** B 291 GLN ** 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 = 0.3260 r_free = 0.3260 target = 0.079577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.062247 restraints weight = 70942.505| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.39 r_work: 0.2810 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 27184 Z= 0.248 Angle : 0.647 13.902 36851 Z= 0.331 Chirality : 0.043 0.186 4246 Planarity : 0.004 0.060 4620 Dihedral : 13.328 171.854 4264 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.52 % Favored : 95.18 % Rotamer: Outliers : 4.96 % Allowed : 20.46 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3317 helix: 0.72 (0.13), residues: 1538 sheet: -0.58 (0.22), residues: 588 loop : -1.30 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 130 TYR 0.023 0.002 TYR W 315 PHE 0.019 0.002 PHE V 126 TRP 0.016 0.002 TRP D 314 HIS 0.011 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 (27182) covalent geometry : angle 0.64718 / 0.33 (36851) hydrogen bonds : bond 0.04403 / 3.00 ( 1269) hydrogen bonds : angle 5.40144 / 3.79 ( 3663) Misc. bond : bond 0.00258 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 127 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8642 (mt0) cc_final: 0.7866 (mt0) REVERT: R 206 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: R 215 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8639 (ptm160) REVERT: V 282 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8558 (t0) REVERT: O 62 ASN cc_start: 0.9259 (t0) cc_final: 0.9025 (t0) REVERT: X 96 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7477 (tt) REVERT: D 292 MET cc_start: 0.7795 (ptt) cc_final: 0.7207 (ptp) REVERT: C 286 MET cc_start: 0.8272 (tpp) cc_final: 0.7839 (tpp) REVERT: B 125 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.9046 (pm20) REVERT: B 197 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8343 (mmtp) REVERT: F 84 MET cc_start: 0.5895 (mpm) cc_final: 0.5503 (mpm) REVERT: F 243 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8748 (tpt) outliers start: 137 outliers final: 50 residues processed: 245 average time/residue: 0.5062 time to fit residues: 148.7264 Evaluate side-chains 178 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 270 VAL Chi-restraints excluded: chain V residue 273 VAL Chi-restraints excluded: chain V residue 282 ASP Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 336 ASP Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 208 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 231 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN B 130 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.063688 restraints weight = 71355.576| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.45 r_work: 0.2828 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27184 Z= 0.162 Angle : 0.572 15.529 36851 Z= 0.296 Chirality : 0.041 0.170 4246 Planarity : 0.004 0.061 4620 Dihedral : 12.789 163.936 4255 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.07 % Favored : 95.66 % Rotamer: Outliers : 4.09 % Allowed : 21.30 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3317 helix: 0.81 (0.13), residues: 1533 sheet: -0.62 (0.22), residues: 585 loop : -1.35 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 130 TYR 0.017 0.001 TYR W 315 PHE 0.016 0.001 PHE E 129 TRP 0.009 0.001 TRP D 314 HIS 0.009 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (27182) covalent geometry : angle 0.57243 / 0.30 (36851) hydrogen bonds : bond 0.03633 / 2.47 ( 1269) hydrogen bonds : angle 5.17285 / 3.63 ( 3663) Misc. bond : bond 0.00217 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 128 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: R 94 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8986 (tm-30) REVERT: R 202 GLN cc_start: 0.8605 (mt0) cc_final: 0.8016 (mt0) REVERT: R 206 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: V 282 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8477 (t0) REVERT: W 158 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8806 (ttm) REVERT: O 62 ASN cc_start: 0.9273 (t0) cc_final: 0.9015 (t0) REVERT: O 189 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8254 (p) REVERT: K 91 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.9025 (mp0) REVERT: X 96 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7506 (tt) REVERT: D 292 MET cc_start: 0.7771 (ptt) cc_final: 0.7143 (ptp) REVERT: C 292 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7600 (pmt-80) REVERT: B 192 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8907 (pp20) REVERT: F 84 MET cc_start: 0.5975 (mpm) cc_final: 0.5554 (mpm) REVERT: F 243 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8800 (tpt) outliers start: 113 outliers final: 46 residues processed: 228 average time/residue: 0.5714 time to fit residues: 154.7104 Evaluate side-chains 178 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 GLU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 211 MET Chi-restraints excluded: chain V residue 282 ASP Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 301 GLN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 71 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 293 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 290 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 188 ASN ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN X 86 HIS ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.081357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.063796 restraints weight = 70716.685| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.36 r_work: 0.2835 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27184 Z= 0.156 Angle : 0.561 16.349 36851 Z= 0.289 Chirality : 0.041 0.168 4246 Planarity : 0.004 0.064 4620 Dihedral : 12.371 159.783 4251 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.19 % Favored : 95.51 % Rotamer: Outliers : 3.95 % Allowed : 22.02 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3317 helix: 0.87 (0.13), residues: 1547 sheet: -0.41 (0.23), residues: 537 loop : -1.39 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 130 TYR 0.016 0.001 TYR W 315 PHE 0.019 0.001 PHE E 129 TRP 0.011 0.001 TRP D 314 HIS 0.008 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (27182) covalent geometry : angle 0.56068 / 0.29 (36851) hydrogen bonds : bond 0.03502 / 2.39 ( 1269) hydrogen bonds : angle 5.03683 / 3.54 ( 3663) Misc. bond : bond 0.00207 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 124 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8536 (mt-10) REVERT: R 94 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8979 (tm-30) REVERT: R 202 GLN cc_start: 0.8616 (mt0) cc_final: 0.8082 (mt0) REVERT: R 206 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: R 215 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8458 (ptm-80) REVERT: V 282 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8479 (t0) REVERT: O 62 ASN cc_start: 0.9300 (t0) cc_final: 0.9028 (t0) REVERT: O 189 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8215 (p) REVERT: K 91 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.9032 (mp0) REVERT: X 96 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7559 (tt) REVERT: D 292 MET cc_start: 0.7794 (ptt) cc_final: 0.7208 (ptp) REVERT: C 292 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7599 (pmt-80) REVERT: B 125 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.9020 (pm20) REVERT: B 192 GLU cc_start: 0.9325 (OUTLIER) cc_final: 0.8913 (pp20) REVERT: B 197 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8456 (mttm) REVERT: F 243 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8760 (tpt) outliers start: 109 outliers final: 50 residues processed: 220 average time/residue: 0.5545 time to fit residues: 145.0240 Evaluate side-chains 182 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 GLU Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 211 MET Chi-restraints excluded: chain V residue 282 ASP Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 315 TYR Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 59 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 332 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 328 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN X 86 HIS ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.080206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.062920 restraints weight = 71148.068| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.41 r_work: 0.2818 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 27184 Z= 0.188 Angle : 0.577 16.048 36851 Z= 0.297 Chirality : 0.041 0.172 4246 Planarity : 0.004 0.059 4620 Dihedral : 12.259 163.352 4251 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.25 % Favored : 95.45 % Rotamer: Outliers : 3.88 % Allowed : 22.17 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3317 helix: 0.89 (0.13), residues: 1548 sheet: -0.42 (0.23), residues: 537 loop : -1.40 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 130 TYR 0.018 0.001 TYR W 315 PHE 0.019 0.001 PHE V 126 TRP 0.007 0.001 TRP X 231 HIS 0.008 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (27182) covalent geometry : angle 0.57724 / 0.30 (36851) hydrogen bonds : bond 0.03597 / 2.44 ( 1269) hydrogen bonds : angle 5.03501 / 3.54 ( 3663) Misc. bond : bond 0.00215 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 118 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8623 (mt0) cc_final: 0.7797 (tt0) REVERT: R 206 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: R 215 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8626 (ptm-80) REVERT: V 282 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8498 (t0) REVERT: W 158 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8777 (ttm) REVERT: W 338 LYS cc_start: 0.8920 (mptt) cc_final: 0.8497 (mptt) REVERT: O 62 ASN cc_start: 0.9305 (t0) cc_final: 0.9022 (t0) REVERT: O 189 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8265 (p) REVERT: O 326 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8119 (mpp) REVERT: K 91 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.9051 (mp0) REVERT: X 96 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7454 (tt) REVERT: D 113 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7248 (mttp) REVERT: D 292 MET cc_start: 0.7768 (ptt) cc_final: 0.7176 (ptp) REVERT: C 292 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7558 (pmt-80) REVERT: B 192 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.8922 (pp20) REVERT: B 197 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8515 (mttm) REVERT: F 130 ARG cc_start: 0.6363 (mmp-170) cc_final: 0.5455 (mmp-170) REVERT: F 223 SER cc_start: 0.8481 (t) cc_final: 0.8128 (p) REVERT: F 243 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8785 (tpt) outliers start: 107 outliers final: 55 residues processed: 208 average time/residue: 0.5251 time to fit residues: 130.5211 Evaluate side-chains 182 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 114 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 261 VAL Chi-restraints excluded: chain V residue 282 ASP Chi-restraints excluded: chain V residue 315 TYR Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 149 ASP Chi-restraints excluded: chain W residue 158 MET Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 315 TYR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 312 CYS Chi-restraints excluded: chain O residue 326 MET Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain X residue 256 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 73 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 318 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 100 optimal weight: 0.0170 chunk 296 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 242 GLN ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN X 86 HIS ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN B 29 HIS B 115 GLN B 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.064559 restraints weight = 70718.591| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.41 r_work: 0.2859 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27184 Z= 0.118 Angle : 0.538 16.831 36851 Z= 0.278 Chirality : 0.040 0.161 4246 Planarity : 0.003 0.061 4620 Dihedral : 12.047 156.305 4250 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.01 % Favored : 95.69 % Rotamer: Outliers : 3.40 % Allowed : 22.67 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3317 helix: 1.15 (0.14), residues: 1501 sheet: -0.36 (0.23), residues: 537 loop : -1.26 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 130 TYR 0.013 0.001 TYR W 315 PHE 0.018 0.001 PHE V 126 TRP 0.012 0.001 TRP D 314 HIS 0.008 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (27182) covalent geometry : angle 0.53827 / 0.28 (36851) hydrogen bonds : bond 0.03204 / 2.19 ( 1269) hydrogen bonds : angle 4.85946 / 3.41 ( 3663) Misc. bond : bond 0.00187 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 120 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8547 (mt0) cc_final: 0.7723 (tt0) REVERT: R 206 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: V 135 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: W 338 LYS cc_start: 0.8909 (mptt) cc_final: 0.8536 (mptt) REVERT: O 62 ASN cc_start: 0.9290 (t0) cc_final: 0.9021 (t0) REVERT: O 189 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7979 (p) REVERT: K 91 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8994 (mp0) REVERT: X 96 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7429 (tt) REVERT: D 292 MET cc_start: 0.7618 (ptt) cc_final: 0.7056 (ptp) REVERT: C 286 MET cc_start: 0.8481 (tpp) cc_final: 0.8026 (tpp) REVERT: C 292 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7508 (pmt-80) REVERT: B 192 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8744 (pp20) REVERT: F 130 ARG cc_start: 0.6147 (mmp-170) cc_final: 0.5940 (mmp-170) REVERT: F 223 SER cc_start: 0.8512 (t) cc_final: 0.8120 (p) REVERT: F 243 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8743 (tpt) outliers start: 94 outliers final: 46 residues processed: 202 average time/residue: 0.5346 time to fit residues: 128.8938 Evaluate side-chains 166 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 112 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 135 GLN Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 261 VAL Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 315 TYR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 312 CYS Chi-restraints excluded: chain O residue 314 ILE Chi-restraints excluded: chain O residue 336 ASP Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 179 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN X 86 HIS ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.062833 restraints weight = 71414.289| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.41 r_work: 0.2814 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27184 Z= 0.186 Angle : 0.579 16.404 36851 Z= 0.295 Chirality : 0.041 0.172 4246 Planarity : 0.004 0.063 4620 Dihedral : 12.063 154.348 4248 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.37 % Favored : 95.33 % Rotamer: Outliers : 3.26 % Allowed : 23.04 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3317 helix: 0.98 (0.13), residues: 1548 sheet: -0.36 (0.23), residues: 537 loop : -1.35 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 130 TYR 0.019 0.001 TYR W 315 PHE 0.023 0.001 PHE V 126 TRP 0.015 0.001 TRP D 314 HIS 0.009 0.001 HIS X 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (27182) covalent geometry : angle 0.57869 / 0.30 (36851) hydrogen bonds : bond 0.03530 / 2.39 ( 1269) hydrogen bonds : angle 4.92316 / 3.46 ( 3663) Misc. bond : bond 0.00214 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 117 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8607 (mt0) cc_final: 0.7813 (tt0) REVERT: R 206 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: W 338 LYS cc_start: 0.8957 (mptt) cc_final: 0.8500 (mptt) REVERT: O 62 ASN cc_start: 0.9318 (t0) cc_final: 0.9052 (t0) REVERT: O 189 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8187 (p) REVERT: K 91 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.9020 (mp0) REVERT: X 96 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7377 (tt) REVERT: X 196 GLN cc_start: 0.8230 (mp10) cc_final: 0.7643 (mm-40) REVERT: D 292 MET cc_start: 0.7737 (ptt) cc_final: 0.7152 (ptp) REVERT: C 284 ASN cc_start: 0.8862 (t0) cc_final: 0.8434 (t0) REVERT: B 192 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8865 (pp20) REVERT: B 197 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8491 (mttm) REVERT: F 223 SER cc_start: 0.8513 (t) cc_final: 0.8127 (p) REVERT: F 243 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8809 (tpt) outliers start: 90 outliers final: 53 residues processed: 197 average time/residue: 0.5456 time to fit residues: 128.1486 Evaluate side-chains 177 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 117 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 261 VAL Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 315 TYR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 312 CYS Chi-restraints excluded: chain O residue 314 ILE Chi-restraints excluded: chain O residue 336 ASP Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 191 LEU Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 319 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN X 86 HIS ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.064125 restraints weight = 71092.509| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.38 r_work: 0.2849 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27184 Z= 0.135 Angle : 0.558 18.048 36851 Z= 0.286 Chirality : 0.041 0.205 4246 Planarity : 0.004 0.061 4620 Dihedral : 12.035 156.284 4248 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.10 % Favored : 95.60 % Rotamer: Outliers : 2.75 % Allowed : 23.51 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 3317 helix: 1.03 (0.14), residues: 1550 sheet: -0.34 (0.23), residues: 543 loop : -1.31 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 130 TYR 0.015 0.001 TYR W 315 PHE 0.022 0.001 PHE V 126 TRP 0.015 0.001 TRP D 314 HIS 0.008 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (27182) covalent geometry : angle 0.55770 / 0.29 (36851) hydrogen bonds : bond 0.03315 / 2.25 ( 1269) hydrogen bonds : angle 4.85658 / 3.41 ( 3663) Misc. bond : bond 0.00197 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 116 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8551 (mt0) cc_final: 0.7756 (tt0) REVERT: R 206 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: W 338 LYS cc_start: 0.8956 (mptt) cc_final: 0.8566 (mptt) REVERT: O 62 ASN cc_start: 0.9296 (t0) cc_final: 0.9039 (t0) REVERT: O 189 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8078 (p) REVERT: K 91 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8992 (mp0) REVERT: X 96 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7324 (tt) REVERT: X 196 GLN cc_start: 0.8185 (mp10) cc_final: 0.7552 (mm-40) REVERT: D 292 MET cc_start: 0.7658 (ptt) cc_final: 0.7076 (ptp) REVERT: C 284 ASN cc_start: 0.8767 (t0) cc_final: 0.8397 (t0) REVERT: C 286 MET cc_start: 0.8357 (tpp) cc_final: 0.7934 (tpp) REVERT: B 125 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8948 (pm20) REVERT: B 192 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8773 (pp20) REVERT: F 223 SER cc_start: 0.8526 (t) cc_final: 0.8114 (p) REVERT: F 243 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8769 (tpt) outliers start: 76 outliers final: 53 residues processed: 182 average time/residue: 0.5177 time to fit residues: 112.1605 Evaluate side-chains 174 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 114 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 261 VAL Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 315 TYR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 312 CYS Chi-restraints excluded: chain O residue 314 ILE Chi-restraints excluded: chain O residue 336 ASP Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 319 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 103 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 333 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 275 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN X 86 HIS ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.064670 restraints weight = 70232.981| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.39 r_work: 0.2878 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27184 Z= 0.135 Angle : 0.556 17.571 36851 Z= 0.284 Chirality : 0.040 0.162 4246 Planarity : 0.003 0.063 4620 Dihedral : 12.001 159.173 4248 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.07 % Favored : 95.66 % Rotamer: Outliers : 2.46 % Allowed : 23.94 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3317 helix: 1.21 (0.14), residues: 1514 sheet: -0.32 (0.23), residues: 543 loop : -1.22 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 130 TYR 0.015 0.001 TYR W 315 PHE 0.024 0.001 PHE V 126 TRP 0.013 0.001 TRP D 314 HIS 0.010 0.001 HIS X 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (27182) covalent geometry : angle 0.55554 / 0.28 (36851) hydrogen bonds : bond 0.03284 / 2.23 ( 1269) hydrogen bonds : angle 4.82304 / 3.39 ( 3663) Misc. bond : bond 0.00194 / 0.13 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6634 Ramachandran restraints generated. 3317 Oldfield, 0 Emsley, 3317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 116 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8646 (mt0) cc_final: 0.7890 (tt0) REVERT: R 206 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7805 (mp10) REVERT: W 338 LYS cc_start: 0.8990 (mptt) cc_final: 0.8636 (mptt) REVERT: O 62 ASN cc_start: 0.9307 (t0) cc_final: 0.9071 (t0) REVERT: O 189 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8176 (p) REVERT: X 96 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7514 (tt) REVERT: D 292 MET cc_start: 0.7900 (ptt) cc_final: 0.7322 (ptp) REVERT: C 284 ASN cc_start: 0.8774 (t0) cc_final: 0.8469 (t0) REVERT: C 286 MET cc_start: 0.8404 (tpp) cc_final: 0.8012 (tpp) REVERT: B 192 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8806 (pp20) REVERT: F 223 SER cc_start: 0.8568 (t) cc_final: 0.8180 (p) REVERT: F 243 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8768 (tpt) outliers start: 68 outliers final: 57 residues processed: 175 average time/residue: 0.5062 time to fit residues: 105.6226 Evaluate side-chains 176 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 114 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 THR Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 215 ARG Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 261 VAL Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 THR Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 315 TYR Chi-restraints excluded: chain O residue 90 THR Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 189 VAL Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 287 ILE Chi-restraints excluded: chain O residue 291 ILE Chi-restraints excluded: chain O residue 311 ILE Chi-restraints excluded: chain O residue 312 CYS Chi-restraints excluded: chain O residue 314 ILE Chi-restraints excluded: chain O residue 326 MET Chi-restraints excluded: chain O residue 336 ASP Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 160 VAL Chi-restraints excluded: chain X residue 227 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 319 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 266 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 247 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN E 34 ASN ** D 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.065293 restraints weight = 70955.695| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.44 r_work: 0.2888 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27184 Z= 0.123 Angle : 0.550 17.195 36851 Z= 0.280 Chirality : 0.040 0.159 4246 Planarity : 0.003 0.063 4620 Dihedral : 11.914 164.554 4248 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 2.54 % Allowed : 23.94 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3317 helix: 1.29 (0.14), residues: 1511 sheet: -0.32 (0.23), residues: 548 loop : -1.16 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 130 TYR 0.014 0.001 TYR W 315 PHE 0.025 0.001 PHE V 126 TRP 0.013 0.001 TRP D 314 HIS 0.009 0.001 HIS X 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (27182) covalent geometry : angle 0.54984 / 0.28 (36851) hydrogen bonds : bond 0.03160 / 2.15 ( 1269) hydrogen bonds : angle 4.76973 / 3.36 ( 3663) Misc. bond : bond 0.00186 / 0.13 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8691.49 seconds wall clock time: 149 minutes 3.21 seconds (8943.21 seconds total)