Starting phenix.real_space_refine on Tue May 5 06:21:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zzr_75014/05_2026/9zzr_75014.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zzr_75014/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9zzr_75014/05_2026/9zzr_75014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zzr_75014/05_2026/9zzr_75014.map" model { file = "/net/cci-nas-00/data/ceres_data/9zzr_75014/05_2026/9zzr_75014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zzr_75014/05_2026/9zzr_75014.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 6.13, per 1000 atoms: 0.23 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: 2.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.98 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: 5.00 Time building geometry restraints manager: 2.76 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: 4163 0.109 - 0.218: 70 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.130 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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= 0.301 Angle : 0.797 18.017 36851 Z= 0.380 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 covalent geometry : bond 0.00603 (27182) covalent geometry : angle 0.79718 (36851) hydrogen bonds : bond 0.20295 ( 1269) hydrogen bonds : angle 7.60314 ( 3663) Misc. bond : bond 0.00657 ( 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 : 0.995 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: 0.5555 time to fit residues: 137.2488 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 : 1.004 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3339 r_free = 0.3339 target = 0.083663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.066189 restraints weight = 70084.231| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.42 r_work: 0.2905 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27184 Z= 0.156 Angle : 0.589 14.035 36851 Z= 0.303 Chirality : 0.041 0.166 4246 Planarity : 0.004 0.062 4620 Dihedral : 14.351 173.213 4311 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.95 % Favored : 95.81 % Rotamer: Outliers : 3.69 % Allowed : 21.55 % Favored : 74.76 % 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: -0.20 (0.14), residues: 3317 helix: 0.92 (0.14), residues: 1487 sheet: -0.31 (0.22), residues: 569 loop : -1.25 (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 0.010 0.001 TRP D 314 HIS 0.012 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00344 (27182) covalent geometry : angle 0.58930 (36851) hydrogen bonds : bond 0.04315 ( 1269) hydrogen bonds : angle 5.60435 ( 3663) Misc. bond : bond 0.00183 ( 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 241 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 139 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 62 ASN cc_start: 0.9031 (t0) cc_final: 0.8816 (t0) REVERT: O 189 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8389 (p) REVERT: C 158 ILE cc_start: 0.8971 (mt) cc_final: 0.8587 (tt) REVERT: C 286 MET cc_start: 0.7949 (tpp) cc_final: 0.7607 (tpp) REVERT: B 105 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9176 (tt) REVERT: B 192 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.9057 (pp20) REVERT: B 197 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8200 (mmtp) REVERT: F 84 MET cc_start: 0.5900 (mpm) cc_final: 0.5464 (mpm) REVERT: F 223 SER cc_start: 0.8660 (t) cc_final: 0.8411 (p) REVERT: F 243 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8659 (tpt) outliers start: 102 outliers final: 34 residues processed: 226 average time/residue: 0.5476 time to fit residues: 147.9726 Evaluate side-chains 173 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 232 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063558 restraints weight = 70612.051| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.39 r_work: 0.2837 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1645 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= 0.188 Angle : 0.591 12.563 36851 Z= 0.305 Chirality : 0.042 0.164 4246 Planarity : 0.004 0.059 4620 Dihedral : 12.815 167.158 4264 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.28 % Favored : 95.45 % Rotamer: Outliers : 4.71 % Allowed : 20.57 % Favored : 74.72 % 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: -0.30 (0.14), residues: 3317 helix: 0.81 (0.13), residues: 1540 sheet: -0.41 (0.23), residues: 541 loop : -1.31 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 130 TYR 0.019 0.001 TYR W 315 PHE 0.017 0.001 PHE V 126 TRP 0.010 0.001 TRP D 314 HIS 0.011 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00428 (27182) covalent geometry : angle 0.59135 (36851) hydrogen bonds : bond 0.03951 ( 1269) hydrogen bonds : angle 5.20496 ( 3663) Misc. bond : bond 0.00217 ( 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 268 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 138 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8555 (mt0) cc_final: 0.7748 (mt0) REVERT: R 206 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: V 135 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8795 (mp10) REVERT: V 282 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8466 (t0) REVERT: O 62 ASN cc_start: 0.9220 (t0) cc_final: 0.8955 (t0) REVERT: O 189 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8289 (p) REVERT: K 91 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.9008 (mp0) REVERT: X 92 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7296 (mp) REVERT: X 96 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7422 (tt) REVERT: D 292 MET cc_start: 0.7679 (ptt) cc_final: 0.7049 (ptp) REVERT: C 286 MET cc_start: 0.8330 (tpp) cc_final: 0.7931 (tpp) REVERT: C 292 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7608 (pmt-80) REVERT: B 192 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9105 (pp20) REVERT: B 197 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8270 (mmtp) REVERT: B 213 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8754 (m-30) REVERT: F 84 MET cc_start: 0.5901 (mpm) cc_final: 0.5495 (mpm) REVERT: F 223 SER cc_start: 0.8706 (t) cc_final: 0.8385 (p) REVERT: F 243 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8731 (tpt) outliers start: 130 outliers final: 44 residues processed: 247 average time/residue: 0.5284 time to fit residues: 155.5141 Evaluate side-chains 185 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 129 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 135 GLN Chi-restraints excluded: chain V residue 270 VAL 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 O residue 39 LYS 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 270 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 92 LEU 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 241 VAL 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 192 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 213 ASP 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: 7.9990 chunk 148 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 231 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.063509 restraints weight = 69923.848| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.34 r_work: 0.2842 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1817 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= 0.172 Angle : 0.572 15.104 36851 Z= 0.294 Chirality : 0.041 0.159 4246 Planarity : 0.004 0.058 4620 Dihedral : 12.392 163.548 4252 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.13 % Favored : 95.60 % Rotamer: Outliers : 4.17 % Allowed : 21.41 % Favored : 74.43 % 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: -0.18 (0.14), residues: 3317 helix: 1.02 (0.14), residues: 1492 sheet: -0.43 (0.23), residues: 537 loop : -1.28 (0.16), residues: 1288 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 0.008 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00396 (27182) covalent geometry : angle 0.57220 (36851) hydrogen bonds : bond 0.03619 ( 1269) hydrogen bonds : angle 5.10331 ( 3663) Misc. bond : bond 0.00212 ( 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 239 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 124 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8947 (tm-30) REVERT: R 202 GLN cc_start: 0.8556 (mt0) cc_final: 0.7864 (mt0) REVERT: R 206 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7517 (mp10) REVERT: R 215 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8389 (ptm-80) REVERT: W 158 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8712 (ttm) REVERT: O 62 ASN cc_start: 0.9247 (t0) cc_final: 0.8977 (t0) REVERT: O 189 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8189 (p) REVERT: O 243 MET cc_start: 0.8919 (tpt) cc_final: 0.8692 (tpt) REVERT: X 96 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7455 (tt) REVERT: D 292 MET cc_start: 0.7647 (ptt) cc_final: 0.7028 (ptp) REVERT: C 286 MET cc_start: 0.8433 (tpp) cc_final: 0.8161 (tpp) REVERT: C 292 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7585 (pmt-80) REVERT: B 192 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9084 (pp20) REVERT: B 213 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8744 (m-30) REVERT: F 84 MET cc_start: 0.5971 (mpm) cc_final: 0.5543 (mpm) REVERT: F 223 SER cc_start: 0.8697 (t) cc_final: 0.8372 (p) REVERT: F 243 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8775 (tpt) outliers start: 115 outliers final: 49 residues processed: 222 average time/residue: 0.5496 time to fit residues: 144.2899 Evaluate side-chains 180 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 121 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 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 82 VAL Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 211 MET Chi-restraints excluded: chain V residue 270 VAL 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 158 MET Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 230 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 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 93 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 118 VAL 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 248 THR 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 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 192 GLU Chi-restraints excluded: chain B residue 213 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 71 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 307 optimal weight: 9.9990 chunk 4 optimal weight: 0.1980 chunk 290 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 101 GLN O 294 HIS O 330 ASN X 86 HIS D 171 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3324 r_free = 0.3324 target = 0.082970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065656 restraints weight = 70531.221| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.45 r_work: 0.2884 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27184 Z= 0.111 Angle : 0.535 15.143 36851 Z= 0.275 Chirality : 0.040 0.151 4246 Planarity : 0.003 0.058 4620 Dihedral : 12.027 157.196 4252 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.92 % Favored : 95.78 % Rotamer: Outliers : 3.48 % Allowed : 22.06 % Favored : 74.47 % 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: -0.03 (0.15), residues: 3317 helix: 1.14 (0.14), residues: 1494 sheet: -0.37 (0.23), residues: 547 loop : -1.21 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 95 TYR 0.012 0.001 TYR W 315 PHE 0.019 0.001 PHE E 129 TRP 0.006 0.001 TRP D 314 HIS 0.008 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00242 (27182) covalent geometry : angle 0.53472 (36851) hydrogen bonds : bond 0.03173 ( 1269) hydrogen bonds : angle 4.88418 ( 3663) Misc. bond : bond 0.00173 ( 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 226 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 130 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8917 (tm-30) REVERT: R 202 GLN cc_start: 0.8508 (mt0) cc_final: 0.8006 (mt0) REVERT: R 206 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: V 135 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8519 (mp10) REVERT: V 282 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8461 (t0) REVERT: O 62 ASN cc_start: 0.9267 (t0) cc_final: 0.8984 (t0) REVERT: O 326 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8043 (mpp) REVERT: X 96 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7452 (tt) REVERT: D 292 MET cc_start: 0.7674 (ptt) cc_final: 0.7095 (ptp) REVERT: C 291 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7612 (p0) REVERT: C 292 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7486 (pmt-80) REVERT: B 192 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8795 (pp20) REVERT: B 213 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8759 (m-30) REVERT: B 261 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: F 84 MET cc_start: 0.5914 (mpm) cc_final: 0.5476 (mpm) REVERT: F 130 ARG cc_start: 0.6170 (mmp-170) cc_final: 0.5940 (mmp-170) REVERT: F 223 SER cc_start: 0.8752 (t) cc_final: 0.8398 (p) REVERT: F 243 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8728 (tpt) outliers start: 96 outliers final: 39 residues processed: 213 average time/residue: 0.5763 time to fit residues: 144.6968 Evaluate side-chains 173 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 94 GLN Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 206 GLN Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 135 GLN 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 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 102 ILE 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 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 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 96 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 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 291 ASP 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 213 ASP Chi-restraints excluded: chain B residue 261 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 328 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 320 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 234 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN X 86 HIS C 340 GLN F 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062458 restraints weight = 71232.577| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.34 r_work: 0.2811 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27184 Z= 0.222 Angle : 0.603 16.350 36851 Z= 0.308 Chirality : 0.042 0.160 4246 Planarity : 0.004 0.057 4620 Dihedral : 11.973 155.336 4247 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.58 % Favored : 95.12 % Rotamer: Outliers : 3.91 % Allowed : 22.35 % 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: -0.20 (0.15), residues: 3317 helix: 0.95 (0.13), residues: 1541 sheet: -0.40 (0.23), residues: 537 loop : -1.35 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 95 TYR 0.022 0.001 TYR W 315 PHE 0.022 0.001 PHE V 126 TRP 0.008 0.001 TRP X 231 HIS 0.009 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00513 (27182) covalent geometry : angle 0.60250 (36851) hydrogen bonds : bond 0.03771 ( 1269) hydrogen bonds : angle 5.04681 ( 3663) Misc. bond : bond 0.00230 ( 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 228 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 120 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8598 (mt0) cc_final: 0.7655 (tt0) REVERT: R 206 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: R 215 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8722 (ptm-80) REVERT: V 282 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8498 (t0) REVERT: W 158 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8763 (ttm) REVERT: O 62 ASN cc_start: 0.9292 (t0) cc_final: 0.8999 (t0) REVERT: O 326 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8133 (mpp) REVERT: X 96 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7427 (tt) REVERT: D 292 MET cc_start: 0.7693 (ptt) cc_final: 0.7043 (ptp) REVERT: C 291 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7885 (p0) REVERT: B 192 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8872 (pp20) REVERT: B 197 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8516 (mttm) REVERT: B 302 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8405 (ptm160) REVERT: F 95 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8379 (mtm110) REVERT: F 223 SER cc_start: 0.8754 (t) cc_final: 0.8399 (p) REVERT: F 243 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8841 (tpt) outliers start: 108 outliers final: 44 residues processed: 213 average time/residue: 0.5498 time to fit residues: 138.5728 Evaluate side-chains 173 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 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 W residue 266 THR Chi-restraints excluded: chain O residue 102 ILE 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 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 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 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 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 291 ASP 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 302 ARG 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 95 ARG Chi-restraints excluded: chain F residue 158 MET 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: 1.9990 chunk 139 optimal weight: 0.9980 chunk 318 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 228 optimal weight: 0.5980 chunk 100 optimal weight: 0.0050 chunk 296 optimal weight: 2.9990 chunk 286 optimal weight: 0.0040 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 101 GLN O 330 ASN X 86 HIS C 340 GLN B 115 GLN B 130 HIS F 94 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.065279 restraints weight = 70565.337| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.43 r_work: 0.2872 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27184 Z= 0.107 Angle : 0.540 16.681 36851 Z= 0.277 Chirality : 0.040 0.155 4246 Planarity : 0.003 0.074 4620 Dihedral : 11.763 155.266 4247 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.95 % Favored : 95.78 % Rotamer: Outliers : 3.30 % Allowed : 22.75 % 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: 0.04 (0.15), residues: 3317 helix: 1.27 (0.14), residues: 1494 sheet: -0.42 (0.23), residues: 551 loop : -1.23 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 130 TYR 0.013 0.001 TYR W 315 PHE 0.015 0.001 PHE V 126 TRP 0.013 0.001 TRP D 314 HIS 0.007 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00233 (27182) covalent geometry : angle 0.53984 (36851) hydrogen bonds : bond 0.03109 ( 1269) hydrogen bonds : angle 4.81869 ( 3663) Misc. bond : bond 0.00170 ( 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 215 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 124 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8528 (mt0) cc_final: 0.7724 (tt0) REVERT: R 206 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: O 62 ASN cc_start: 0.9284 (t0) cc_final: 0.9018 (t0) REVERT: O 101 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: O 189 VAL cc_start: 0.8412 (OUTLIER) cc_final: 0.8203 (p) REVERT: X 96 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7437 (tt) REVERT: D 292 MET cc_start: 0.7706 (ptt) cc_final: 0.7142 (ptp) REVERT: C 185 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: C 284 ASN cc_start: 0.8727 (t0) cc_final: 0.8272 (t0) REVERT: C 286 MET cc_start: 0.8514 (tpp) cc_final: 0.8130 (tpp) REVERT: C 292 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7559 (pmt-80) REVERT: B 105 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9223 (tt) REVERT: B 192 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8777 (pp20) REVERT: B 213 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8663 (m-30) REVERT: F 84 MET cc_start: 0.6056 (OUTLIER) cc_final: 0.5804 (mpm) REVERT: F 95 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8304 (mtm110) REVERT: F 223 SER cc_start: 0.8757 (t) cc_final: 0.8387 (p) REVERT: F 243 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8808 (tpt) outliers start: 91 outliers final: 47 residues processed: 202 average time/residue: 0.5638 time to fit residues: 134.6172 Evaluate side-chains 178 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain V residue 25 ILE 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 101 GLN 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 133 LYS Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 96 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 248 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 185 GLU 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 105 LEU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 213 ASP 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 84 MET Chi-restraints excluded: chain F residue 95 ARG 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: 3.9990 chunk 172 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 GLN O 330 ASN X 86 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN F 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.062621 restraints weight = 71273.868| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.35 r_work: 0.2821 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27184 Z= 0.203 Angle : 0.592 16.168 36851 Z= 0.302 Chirality : 0.042 0.157 4246 Planarity : 0.004 0.085 4620 Dihedral : 11.818 161.721 4247 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.46 % Favored : 95.24 % Rotamer: Outliers : 3.40 % Allowed : 22.56 % 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: -0.10 (0.15), residues: 3317 helix: 1.06 (0.14), residues: 1542 sheet: -0.33 (0.22), residues: 547 loop : -1.35 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG F 130 TYR 0.019 0.001 TYR W 315 PHE 0.025 0.001 PHE V 126 TRP 0.010 0.001 TRP D 314 HIS 0.009 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00473 (27182) covalent geometry : angle 0.59174 (36851) hydrogen bonds : bond 0.03629 ( 1269) hydrogen bonds : angle 4.96532 ( 3663) Misc. bond : bond 0.00236 ( 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 208 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 114 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8574 (mt0) cc_final: 0.7781 (tt0) REVERT: R 206 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: O 62 ASN cc_start: 0.9295 (t0) cc_final: 0.9025 (t0) REVERT: X 96 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7328 (tt) REVERT: D 292 MET cc_start: 0.7736 (ptt) cc_final: 0.7141 (ptp) REVERT: C 284 ASN cc_start: 0.8889 (t0) cc_final: 0.8377 (t0) REVERT: C 286 MET cc_start: 0.8510 (tpp) cc_final: 0.8242 (tpp) REVERT: B 192 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8867 (pp20) REVERT: B 197 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8513 (mttm) REVERT: F 95 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8354 (mtm110) REVERT: F 223 SER cc_start: 0.8736 (t) cc_final: 0.8359 (p) REVERT: F 243 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8818 (tpt) outliers start: 94 outliers final: 54 residues processed: 196 average time/residue: 0.5716 time to fit residues: 132.4852 Evaluate side-chains 173 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 113 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain R residue 330 ASN Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain V residue 143 THR Chi-restraints excluded: chain V residue 261 VAL Chi-restraints excluded: chain V residue 270 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 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 133 LYS Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 270 VAL Chi-restraints excluded: chain X residue 93 VAL Chi-restraints excluded: chain X residue 96 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 113 LYS Chi-restraints excluded: chain D residue 202 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 288 THR 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 110 SER 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 95 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 125 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 261 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 295 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 101 GLN O 242 GLN O 330 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065118 restraints weight = 70666.822| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.40 r_work: 0.2876 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2398 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= 0.115 Angle : 0.546 17.161 36851 Z= 0.279 Chirality : 0.040 0.158 4246 Planarity : 0.003 0.065 4620 Dihedral : 11.687 165.918 4247 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.89 % Favored : 95.84 % Rotamer: Outliers : 2.54 % Allowed : 23.54 % 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: 0.11 (0.15), residues: 3317 helix: 1.31 (0.14), residues: 1493 sheet: -0.37 (0.23), residues: 539 loop : -1.19 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 130 TYR 0.013 0.001 TYR W 315 PHE 0.019 0.001 PHE V 126 TRP 0.016 0.001 TRP D 314 HIS 0.008 0.001 HIS C 250 Details of bonding type rmsd covalent geometry : bond 0.00257 (27182) covalent geometry : angle 0.54553 (36851) hydrogen bonds : bond 0.03090 ( 1269) hydrogen bonds : angle 4.78637 ( 3663) Misc. bond : bond 0.00179 ( 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 188 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 118 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8484 (mt0) cc_final: 0.7681 (tt0) REVERT: R 206 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: O 62 ASN cc_start: 0.9285 (t0) cc_final: 0.9035 (t0) REVERT: O 189 VAL cc_start: 0.8448 (p) cc_final: 0.8240 (p) REVERT: X 96 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7415 (tt) REVERT: D 292 MET cc_start: 0.7774 (ptt) cc_final: 0.7270 (ptp) REVERT: C 284 ASN cc_start: 0.8697 (t0) cc_final: 0.8274 (t0) REVERT: C 286 MET cc_start: 0.8490 (tpp) cc_final: 0.8138 (tpp) REVERT: B 192 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8747 (pp20) REVERT: F 223 SER cc_start: 0.8789 (t) cc_final: 0.8382 (p) REVERT: F 243 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8785 (tpt) outliers start: 70 outliers final: 46 residues processed: 181 average time/residue: 0.5659 time to fit residues: 121.2276 Evaluate side-chains 163 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 90 THR 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 143 THR 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 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 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 227 LEU 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 280 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 156 VAL 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 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 158 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 103 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 333 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 330 ASN E 34 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 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 = 0.3328 r_free = 0.3328 target = 0.082438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065332 restraints weight = 70397.372| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.37 r_work: 0.2893 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2453 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= 0.126 Angle : 0.554 17.262 36851 Z= 0.282 Chirality : 0.040 0.205 4246 Planarity : 0.004 0.090 4620 Dihedral : 11.593 167.703 4247 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.95 % Favored : 95.84 % Rotamer: Outliers : 2.35 % Allowed : 23.94 % 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: 0.15 (0.15), residues: 3317 helix: 1.31 (0.14), residues: 1512 sheet: -0.31 (0.23), residues: 539 loop : -1.17 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG F 130 TYR 0.015 0.001 TYR W 315 PHE 0.026 0.001 PHE V 126 TRP 0.011 0.001 TRP D 314 HIS 0.009 0.001 HIS X 98 Details of bonding type rmsd covalent geometry : bond 0.00284 (27182) covalent geometry : angle 0.55414 (36851) hydrogen bonds : bond 0.03150 ( 1269) hydrogen bonds : angle 4.76356 ( 3663) Misc. bond : bond 0.00185 ( 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: 65 poor density : 119 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 202 GLN cc_start: 0.8558 (mt0) cc_final: 0.7773 (tt0) REVERT: R 206 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: O 62 ASN cc_start: 0.9296 (t0) cc_final: 0.9054 (t0) REVERT: X 96 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7454 (tt) REVERT: D 292 MET cc_start: 0.7718 (ptt) cc_final: 0.7184 (ptp) REVERT: C 284 ASN cc_start: 0.8714 (t0) cc_final: 0.8259 (t0) REVERT: C 286 MET cc_start: 0.8510 (tpp) cc_final: 0.8238 (tpp) REVERT: B 192 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8765 (pp20) REVERT: F 223 SER cc_start: 0.8741 (t) cc_final: 0.8346 (p) REVERT: F 243 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8784 (tpt) outliers start: 65 outliers final: 51 residues processed: 173 average time/residue: 0.5728 time to fit residues: 117.5864 Evaluate side-chains 169 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 90 THR 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 V residue 25 ILE Chi-restraints excluded: chain V residue 143 THR 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 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 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 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 93 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 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 288 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 110 SER 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 125 MET Chi-restraints excluded: chain F residue 158 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 266 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 307 optimal weight: 0.0980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.065210 restraints weight = 70109.227| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.40 r_work: 0.2895 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27184 Z= 0.132 Angle : 0.559 17.056 36851 Z= 0.285 Chirality : 0.040 0.177 4246 Planarity : 0.003 0.066 4620 Dihedral : 11.586 169.152 4247 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.04 % Favored : 95.75 % Rotamer: Outliers : 2.54 % Allowed : 23.87 % 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: 0.17 (0.15), residues: 3317 helix: 1.33 (0.14), residues: 1512 sheet: -0.29 (0.23), residues: 539 loop : -1.17 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG F 130 TYR 0.015 0.001 TYR W 315 PHE 0.028 0.001 PHE V 126 TRP 0.009 0.001 TRP D 314 HIS 0.008 0.001 HIS X 98 Details of bonding type rmsd covalent geometry : bond 0.00301 (27182) covalent geometry : angle 0.55856 (36851) hydrogen bonds : bond 0.03158 ( 1269) hydrogen bonds : angle 4.75283 ( 3663) Misc. bond : bond 0.00184 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8898.54 seconds wall clock time: 152 minutes 20.73 seconds (9140.73 seconds total)