Starting phenix.real_space_refine on Thu Aug 6 10:22:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2d_44104/08_2026/9b2d_44104_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2d_44104/08_2026/9b2d_44104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b2d_44104/08_2026/9b2d_44104_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2d_44104/08_2026/9b2d_44104_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b2d_44104/08_2026/9b2d_44104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2d_44104/08_2026/9b2d_44104.map" } resolution = 2.4 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= 0.001 sd= 0.040 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: 8 Type Number sf(0) Gaussians Al 6 5.89 5 P 36 5.49 5 Mg 6 5.21 5 S 102 5.16 5 C 9150 2.51 5 N 2586 2.21 5 O 2862 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14766 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "E" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "F" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2349 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain breaks: 1 Chain: "K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 480 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.55, per 1000 atoms: 0.24 Number of scatterers: 14766 At special positions: 0 Unit cell: (114.92, 113.56, 166.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 36 15.00 Al 6 13.00 Mg 6 11.99 F 18 9.00 O 2862 8.00 N 2586 7.00 C 9150 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 454.9 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 18 sheets defined 50.9% alpha, 16.5% beta 0 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.806A pdb=" N LEU C 86 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.584A pdb=" N VAL C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.555A pdb=" N VAL C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 127 through 140 removed outlier: 3.921A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 164 through 172 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.518A pdb=" N LEU C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 204 No H-bonds generated for 'chain 'C' and resid 203 through 204' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.620A pdb=" N ILE C 208 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 236 removed outlier: 3.922A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 246 Processing helix chain 'C' and resid 254 through 270 removed outlier: 4.301A pdb=" N LEU C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 removed outlier: 4.377A pdb=" N THR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.736A pdb=" N MET C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.567A pdb=" N VAL D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 128 through 140 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.523A pdb=" N SER D 155 " --> pdb=" O HIS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 171 Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.576A pdb=" N LEU D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.520A pdb=" N ILE D 208 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 236 removed outlier: 4.131A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 254 through 270 removed outlier: 4.168A pdb=" N LEU D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 removed outlier: 4.392A pdb=" N THR D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 318 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.645A pdb=" N MET D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 354 " --> pdb=" O MET D 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.599A pdb=" N LEU E 86 " --> pdb=" O ILE E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 103 removed outlier: 3.796A pdb=" N VAL E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 removed outlier: 3.524A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 Processing helix chain 'E' and resid 125 through 140 removed outlier: 3.557A pdb=" N ALA E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 164 through 172 Processing helix chain 'E' and resid 190 through 202 removed outlier: 3.553A pdb=" N LEU E 194 " --> pdb=" O GLY E 190 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL E 200 " --> pdb=" O HIS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 204 No H-bonds generated for 'chain 'E' and resid 203 through 204' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 225 through 236 removed outlier: 3.810A pdb=" N LEU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 254 through 270 removed outlier: 4.188A pdb=" N LEU E 262 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 270 " --> pdb=" O ALA E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 removed outlier: 4.312A pdb=" N THR E 288 " --> pdb=" O ALA E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 318 Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.541A pdb=" N MET E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 Processing helix chain 'F' and resid 92 through 103 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.538A pdb=" N VAL F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 119 Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 164 through 172 Processing helix chain 'F' and resid 190 through 202 removed outlier: 3.547A pdb=" N LEU F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 200 " --> pdb=" O HIS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 204 No H-bonds generated for 'chain 'F' and resid 203 through 204' Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 225 through 236 removed outlier: 4.124A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL F 230 " --> pdb=" O PRO F 226 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER F 231 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE F 236 " --> pdb=" O ILE F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 254 through 270 removed outlier: 4.233A pdb=" N LEU F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 290 removed outlier: 4.327A pdb=" N THR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 294 No H-bonds generated for 'chain 'F' and resid 292 through 294' Processing helix chain 'F' and resid 295 through 318 removed outlier: 3.535A pdb=" N MET F 301 " --> pdb=" O SER F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 354 removed outlier: 3.812A pdb=" N MET F 350 " --> pdb=" O GLY F 346 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 351 " --> pdb=" O GLY F 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.826A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.599A pdb=" N GLU A 120 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.591A pdb=" N LEU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 204 No H-bonds generated for 'chain 'A' and resid 203 through 204' Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.882A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.662A pdb=" N ASN A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 270 removed outlier: 4.302A pdb=" N LEU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 297 through 318 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.039A pdb=" N MET A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.617A pdb=" N LYS B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.569A pdb=" N VAL B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.590A pdb=" N VAL B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.585A pdb=" N CYS B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 204 No H-bonds generated for 'chain 'B' and resid 203 through 204' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 225 through 236 removed outlier: 4.119A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 254 through 270 removed outlier: 4.261A pdb=" N LEU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.515A pdb=" N ARG B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.662A pdb=" N MET B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.754A pdb=" N LYS B 214 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N VAL B 278 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 216 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ASP B 280 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE B 218 " --> pdb=" O ASP B 280 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 180 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N LEU B 358 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU B 182 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE B 360 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B 184 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N LYS B 362 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 357 " --> pdb=" O VAL B 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 391 through 393 removed outlier: 6.459A pdb=" N ARG C 357 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 277 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N THR C 324 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL C 279 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU C 216 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP C 280 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 218 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AA5, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA6, first strand: chain 'D' and resid 391 through 393 removed outlier: 6.477A pdb=" N ARG D 357 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE D 180 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU D 358 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU D 182 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE D 360 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE D 184 " --> pdb=" O PHE D 360 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N LYS D 362 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR D 181 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ASN D 325 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 183 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER D 275 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL D 322 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 277 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N THR D 324 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL D 279 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS D 214 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE D 277 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU D 216 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 279 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE D 218 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AA8, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'E' and resid 391 through 393 removed outlier: 6.501A pdb=" N ARG E 357 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE E 180 " --> pdb=" O THR E 356 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU E 358 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU E 182 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE E 360 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE E 184 " --> pdb=" O PHE E 360 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N LYS E 362 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR E 181 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASN E 325 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU E 183 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E 277 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N THR E 324 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 279 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU E 216 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASP E 280 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 218 " --> pdb=" O ASP E 280 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS E 215 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA E 250 " --> pdb=" O CYS E 215 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR E 217 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AB2, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AB3, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.442A pdb=" N CYS F 215 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ALA F 250 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR F 217 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS F 214 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE F 277 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU F 216 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL F 279 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE F 218 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER F 275 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL F 322 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE F 277 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR F 324 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL F 279 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR F 181 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASN F 325 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU F 183 " --> pdb=" O ASN F 325 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE F 180 " --> pdb=" O THR F 356 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LEU F 358 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU F 182 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE F 360 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N PHE F 184 " --> pdb=" O PHE F 360 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N LYS F 362 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG F 357 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 327 through 329 Processing sheet with id=AB5, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AB6, first strand: chain 'A' and resid 391 through 393 removed outlier: 3.613A pdb=" N CYS A 370 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 357 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 180 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU A 358 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A 182 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE A 360 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 184 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N LYS A 362 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR A 181 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ASN A 325 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 183 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER A 275 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL A 322 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 277 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR A 324 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 279 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A 214 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL A 278 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 216 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ASP A 280 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 218 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS A 215 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ALA A 250 " --> pdb=" O CYS A 215 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR A 217 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AB8, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'B' and resid 327 through 329 611 hydrogen bonds defined for protein. 1710 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3906 1.33 - 1.45: 2482 1.45 - 1.57: 8390 1.57 - 1.70: 83 1.70 - 1.82: 156 Bond restraints: 15017 Sorted by residual: bond pdb=" C3' DT K 15 " pdb=" C2' DT K 15 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.48e+01 bond pdb=" C3' DT K 18 " pdb=" C2' DT K 18 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DT K 6 " pdb=" C2' DT K 6 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT K 21 " pdb=" C2' DT K 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DT K 12 " pdb=" C2' DT K 12 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 ... (remaining 15012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 19708 1.84 - 3.67: 565 3.67 - 5.51: 65 5.51 - 7.35: 26 7.35 - 9.18: 2 Bond angle restraints: 20366 Sorted by residual: angle pdb=" N3 DT K 22 " pdb=" C4 DT K 22 " pdb=" O4 DT K 22 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT K 2 " pdb=" C4 DT K 2 " pdb=" O4 DT K 2 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT K 24 " pdb=" C4 DT K 24 " pdb=" O4 DT K 24 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT K 3 " pdb=" C4 DT K 3 " pdb=" O4 DT K 3 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT K 9 " pdb=" C4 DT K 9 " pdb=" O4 DT K 9 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 20361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 8466 34.06 - 68.11: 523 68.11 - 102.17: 26 102.17 - 136.22: 5 136.22 - 170.28: 13 Dihedral angle restraints: 9033 sinusoidal: 3771 harmonic: 5262 Sorted by residual: dihedral pdb=" O1B ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PB ADP B 501 " pdb=" PA ADP B 501 " ideal model delta sinusoidal sigma weight residual 300.00 129.72 170.28 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 131.60 168.40 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 133.77 166.23 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 9030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1334 0.030 - 0.060: 642 0.060 - 0.089: 196 0.089 - 0.119: 141 0.119 - 0.149: 33 Chirality restraints: 2346 Sorted by residual: chirality pdb=" CA ILE E 387 " pdb=" N ILE E 387 " pdb=" C ILE E 387 " pdb=" CB ILE E 387 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE D 387 " pdb=" N ILE D 387 " pdb=" C ILE D 387 " pdb=" CB ILE D 387 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE F 124 " pdb=" N ILE F 124 " pdb=" C ILE F 124 " pdb=" CB ILE F 124 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2343 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 297 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C SER A 297 " 0.056 2.00e-02 2.50e+03 pdb=" O SER A 297 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA A 298 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 239 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO A 240 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 225 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO C 226 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " 0.023 5.00e-02 4.00e+02 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 46 2.52 - 3.12: 9662 3.12 - 3.71: 20489 3.71 - 4.31: 30851 4.31 - 4.90: 51373 Nonbonded interactions: 112421 Sorted by model distance: nonbonded pdb=" O2B ADP D 501 " pdb=" F1 AF3 D 502 " model vdw 1.929 2.990 nonbonded pdb=" O2B ADP E 501 " pdb=" F1 AF3 E 502 " model vdw 1.957 2.990 nonbonded pdb=" O2B ADP C 501 " pdb=" F3 AF3 C 502 " model vdw 1.997 2.990 nonbonded pdb=" O2B ADP F 501 " pdb=" F1 AF3 F 502 " model vdw 2.003 2.990 nonbonded pdb=" O1B ADP B 501 " pdb="MG MG B 503 " model vdw 2.010 2.170 ... (remaining 112416 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.430 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.011 0.602 15021 Z= 1.014 Angle : 0.711 9.185 20366 Z= 0.417 Chirality : 0.044 0.149 2346 Planarity : 0.004 0.063 2532 Dihedral : 20.733 170.279 5649 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.66 % Allowed : 21.85 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.27 (0.19), residues: 1830 helix: 0.30 (0.19), residues: 810 sheet: 2.63 (0.35), residues: 210 loop : -1.46 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 225 TYR 0.010 0.002 TYR C 217 PHE 0.011 0.002 PHE B 385 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.25 (15017) covalent geometry : angle 0.71090 / 0.42 (20366) hydrogen bonds : bond 0.20116 / 13.31 ( 611) hydrogen bonds : angle 5.68443 / 3.96 ( 1710) Misc. bond : bond 0.60222 / 30.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.532 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 39 residues processed: 197 average time/residue: 0.7332 time to fit residues: 155.9908 Evaluate side-chains 196 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 188 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 383 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 267 GLN ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.149520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.108179 restraints weight = 13043.549| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.35 r_work: 0.2922 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15021 Z= 0.266 Angle : 0.853 9.029 20366 Z= 0.447 Chirality : 0.053 0.354 2346 Planarity : 0.006 0.077 2532 Dihedral : 17.136 165.640 2370 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.25 % Allowed : 19.79 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.45 (0.19), residues: 1830 helix: 0.05 (0.18), residues: 864 sheet: 2.75 (0.35), residues: 210 loop : -1.61 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 293 TYR 0.012 0.002 TYR B 217 PHE 0.013 0.002 PHE A 385 HIS 0.005 0.002 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.27 (15017) covalent geometry : angle 0.85310 / 0.45 (20366) hydrogen bonds : bond 0.09549 / 6.43 ( 611) hydrogen bonds : angle 4.78143 / 3.34 ( 1710) Misc. bond : bond 0.00110 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: C 142 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7886 (mtm) REVERT: C 152 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7740 (ttm) REVERT: C 207 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7601 (p0) REVERT: C 343 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8954 (pttp) REVERT: D 216 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8751 (tt) REVERT: D 287 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7891 (mtt-85) REVERT: E 115 ARG cc_start: 0.7907 (ttt-90) cc_final: 0.7696 (ttt-90) REVERT: E 138 ARG cc_start: 0.7586 (ttp-110) cc_final: 0.7318 (ttt180) REVERT: F 115 ARG cc_start: 0.7683 (ttt-90) cc_final: 0.7375 (ttt-90) REVERT: F 364 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.7042 (ptpp) REVERT: A 93 MET cc_start: 0.5142 (OUTLIER) cc_final: 0.4043 (tmt) REVERT: A 204 ILE cc_start: 0.6253 (OUTLIER) cc_final: 0.6026 (mp) REVERT: B 142 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7343 (mtm) outliers start: 64 outliers final: 26 residues processed: 204 average time/residue: 0.7511 time to fit residues: 164.3480 Evaluate side-chains 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 287 ARG Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 316 GLN E 267 GLN F 166 ASN A 245 ASN B 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.154056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113525 restraints weight = 13284.382| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.33 r_work: 0.3010 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15021 Z= 0.168 Angle : 0.673 7.319 20366 Z= 0.348 Chirality : 0.046 0.246 2346 Planarity : 0.004 0.044 2532 Dihedral : 16.479 157.383 2328 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.78 % Allowed : 20.05 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -0.06 (0.20), residues: 1830 helix: 0.32 (0.18), residues: 870 sheet: 2.56 (0.31), residues: 270 loop : -1.60 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.008 0.001 TYR B 253 PHE 0.012 0.001 PHE B 184 HIS 0.003 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (15017) covalent geometry : angle 0.67309 / 0.35 (20366) hydrogen bonds : bond 0.06557 / 4.43 ( 611) hydrogen bonds : angle 4.33036 / 3.03 ( 1710) Misc. bond : bond 0.00108 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.5188 (mmp) REVERT: C 116 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7116 (ttpt) REVERT: C 152 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7677 (ttm) REVERT: C 343 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8914 (pttp) REVERT: D 115 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7845 (ttt90) REVERT: D 126 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.6047 (mm-30) REVERT: D 216 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8649 (tt) REVERT: E 115 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.7689 (ttt-90) REVERT: E 138 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.7350 (ttt180) REVERT: F 364 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6922 (ptpp) REVERT: A 93 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4070 (tmt) REVERT: A 204 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5879 (mp) outliers start: 57 outliers final: 20 residues processed: 203 average time/residue: 0.7130 time to fit residues: 155.8454 Evaluate side-chains 186 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 74 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 316 GLN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111163 restraints weight = 13109.123| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.32 r_work: 0.2973 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15021 Z= 0.202 Angle : 0.731 7.568 20366 Z= 0.381 Chirality : 0.048 0.290 2346 Planarity : 0.005 0.047 2532 Dihedral : 16.509 156.506 2324 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.72 % Allowed : 19.92 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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 (0.19), residues: 1830 helix: 0.32 (0.18), residues: 864 sheet: 2.97 (0.35), residues: 210 loop : -1.55 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.010 0.002 TYR C 217 PHE 0.012 0.002 PHE B 184 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.20 (15017) covalent geometry : angle 0.73080 / 0.38 (20366) hydrogen bonds : bond 0.07642 / 5.16 ( 611) hydrogen bonds : angle 4.42794 / 3.09 ( 1710) Misc. bond : bond 0.00127 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7107 (ttpt) REVERT: C 152 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7708 (ttm) REVERT: C 207 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7522 (p0) REVERT: C 293 ARG cc_start: 0.6972 (mpt180) cc_final: 0.6382 (tmm160) REVERT: C 343 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8937 (pttp) REVERT: D 115 ARG cc_start: 0.8229 (ttt180) cc_final: 0.7889 (ttt90) REVERT: D 126 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5976 (mm-30) REVERT: D 216 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8712 (tt) REVERT: D 343 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8770 (ptpt) REVERT: E 138 ARG cc_start: 0.7604 (ttp-110) cc_final: 0.7375 (ttt180) REVERT: F 93 MET cc_start: 0.5262 (mpt) cc_final: 0.4375 (mtm) REVERT: F 364 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6971 (ptpp) REVERT: A 93 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.4027 (tmt) REVERT: A 204 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5906 (mp) outliers start: 56 outliers final: 25 residues processed: 205 average time/residue: 0.7365 time to fit residues: 162.7999 Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.0270 chunk 84 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.156474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116101 restraints weight = 13290.736| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.35 r_work: 0.3049 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15021 Z= 0.136 Angle : 0.613 7.012 20366 Z= 0.313 Chirality : 0.044 0.210 2346 Planarity : 0.004 0.042 2532 Dihedral : 16.187 157.603 2323 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.05 % Allowed : 20.78 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.19 (0.20), residues: 1830 helix: 0.56 (0.19), residues: 870 sheet: 2.73 (0.31), residues: 270 loop : -1.55 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.007 0.001 TYR C 253 PHE 0.010 0.001 PHE B 184 HIS 0.002 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.14 (15017) covalent geometry : angle 0.61260 / 0.31 (20366) hydrogen bonds : bond 0.05322 / 3.60 ( 611) hydrogen bonds : angle 4.09024 / 2.86 ( 1710) Misc. bond : bond 0.00094 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.5066 (mmp) REVERT: C 293 ARG cc_start: 0.6721 (mpt180) cc_final: 0.6194 (tmm160) REVERT: D 115 ARG cc_start: 0.8184 (ttt180) cc_final: 0.7810 (ttt90) REVERT: D 216 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8625 (tt) REVERT: E 115 ARG cc_start: 0.7910 (ttt-90) cc_final: 0.7701 (ttt-90) REVERT: E 138 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.7386 (ttt180) REVERT: F 85 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6216 (mttm) REVERT: F 93 MET cc_start: 0.5215 (mpt) cc_final: 0.4366 (mtm) REVERT: F 115 ARG cc_start: 0.7651 (ttt-90) cc_final: 0.6922 (ttm-80) REVERT: F 122 LYS cc_start: 0.5283 (OUTLIER) cc_final: 0.4601 (ttmt) REVERT: F 364 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6832 (ptpp) REVERT: A 93 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.4020 (tmt) REVERT: A 204 ILE cc_start: 0.6031 (OUTLIER) cc_final: 0.5762 (mp) REVERT: B 142 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7195 (mtm) outliers start: 46 outliers final: 16 residues processed: 189 average time/residue: 0.8328 time to fit residues: 169.2350 Evaluate side-chains 180 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 66 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.156029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116070 restraints weight = 13331.573| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.30 r_work: 0.3057 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15021 Z= 0.143 Angle : 0.622 7.178 20366 Z= 0.317 Chirality : 0.044 0.220 2346 Planarity : 0.004 0.040 2532 Dihedral : 16.028 157.705 2319 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.92 % Allowed : 20.85 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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 (0.20), residues: 1830 helix: 0.66 (0.19), residues: 870 sheet: 2.78 (0.31), residues: 270 loop : -1.49 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.007 0.001 TYR B 253 PHE 0.010 0.001 PHE B 184 HIS 0.003 0.001 HIS D 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (15017) covalent geometry : angle 0.62152 / 0.32 (20366) hydrogen bonds : bond 0.05516 / 3.72 ( 611) hydrogen bonds : angle 4.04958 / 2.83 ( 1710) Misc. bond : bond 0.00094 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5596 (OUTLIER) cc_final: 0.5209 (mmp) REVERT: C 293 ARG cc_start: 0.6891 (mpt180) cc_final: 0.6307 (tmm160) REVERT: D 115 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7999 (ttt90) REVERT: D 216 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8648 (tt) REVERT: E 138 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.7464 (ttt180) REVERT: F 85 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6302 (mttm) REVERT: F 93 MET cc_start: 0.5304 (mpt) cc_final: 0.4459 (mtm) REVERT: F 115 ARG cc_start: 0.7689 (ttt-90) cc_final: 0.7023 (ttm-80) REVERT: F 122 LYS cc_start: 0.5384 (OUTLIER) cc_final: 0.4610 (ttmt) REVERT: F 216 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8072 (tt) REVERT: F 364 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6887 (ptpp) REVERT: A 93 MET cc_start: 0.5159 (OUTLIER) cc_final: 0.4028 (tmt) REVERT: A 204 ILE cc_start: 0.6127 (OUTLIER) cc_final: 0.5829 (mp) REVERT: B 142 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7245 (mtm) outliers start: 44 outliers final: 20 residues processed: 188 average time/residue: 0.7603 time to fit residues: 153.8523 Evaluate side-chains 180 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 383 CYS Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 26 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.155110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115796 restraints weight = 13225.979| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.24 r_work: 0.3047 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15021 Z= 0.154 Angle : 0.643 7.233 20366 Z= 0.329 Chirality : 0.045 0.231 2346 Planarity : 0.004 0.040 2532 Dihedral : 16.070 158.004 2318 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.79 % Allowed : 21.12 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.29 (0.20), residues: 1830 helix: 0.65 (0.19), residues: 870 sheet: 2.77 (0.31), residues: 270 loop : -1.50 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.008 0.001 TYR C 217 PHE 0.010 0.001 PHE B 184 HIS 0.003 0.001 HIS D 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (15017) covalent geometry : angle 0.64257 / 0.33 (20366) hydrogen bonds : bond 0.05965 / 4.03 ( 611) hydrogen bonds : angle 4.09977 / 2.86 ( 1710) Misc. bond : bond 0.00105 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5276 (mmp) REVERT: C 293 ARG cc_start: 0.6987 (mpt180) cc_final: 0.6439 (tmm160) REVERT: D 115 ARG cc_start: 0.8207 (ttt180) cc_final: 0.7997 (ttt90) REVERT: D 216 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8667 (tt) REVERT: E 116 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7072 (pttp) REVERT: E 138 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7475 (ttt180) REVERT: E 216 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8492 (tt) REVERT: F 85 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6324 (mttm) REVERT: F 93 MET cc_start: 0.5332 (mpt) cc_final: 0.4506 (mtm) REVERT: F 122 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.4629 (ttmt) REVERT: F 216 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8069 (tt) REVERT: F 364 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6898 (ptpp) REVERT: A 93 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.4035 (tmt) REVERT: A 204 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5849 (mp) REVERT: B 115 ARG cc_start: 0.7102 (tmm-80) cc_final: 0.6737 (ttt-90) REVERT: B 142 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7267 (mtm) outliers start: 42 outliers final: 22 residues processed: 187 average time/residue: 0.7372 time to fit residues: 147.9268 Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 383 CYS Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 151 optimal weight: 20.0000 chunk 171 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.154577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114871 restraints weight = 13330.240| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.27 r_work: 0.3033 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15021 Z= 0.158 Angle : 0.654 7.244 20366 Z= 0.336 Chirality : 0.045 0.234 2346 Planarity : 0.004 0.040 2532 Dihedral : 16.109 157.919 2318 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.05 % Allowed : 20.78 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1830 helix: 0.66 (0.19), residues: 864 sheet: 2.77 (0.31), residues: 270 loop : -1.52 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.008 0.001 TYR C 217 PHE 0.010 0.001 PHE B 184 HIS 0.003 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (15017) covalent geometry : angle 0.65356 / 0.34 (20366) hydrogen bonds : bond 0.06085 / 4.11 ( 611) hydrogen bonds : angle 4.20315 / 2.90 ( 1710) Misc. bond : bond 0.00108 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5698 (OUTLIER) cc_final: 0.5299 (mmp) REVERT: C 207 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7425 (p0) REVERT: C 293 ARG cc_start: 0.7034 (mpt180) cc_final: 0.6477 (tmm160) REVERT: D 216 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8672 (tt) REVERT: E 116 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7083 (pttp) REVERT: E 138 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7500 (ttt180) REVERT: E 216 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8496 (tt) REVERT: F 85 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6340 (mttm) REVERT: F 115 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7249 (ttt-90) REVERT: F 122 LYS cc_start: 0.5387 (OUTLIER) cc_final: 0.4635 (ttmt) REVERT: F 216 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8086 (tt) REVERT: F 364 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6921 (ptpp) REVERT: A 93 MET cc_start: 0.5249 (OUTLIER) cc_final: 0.4106 (tmt) REVERT: A 204 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5893 (mp) REVERT: B 142 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7277 (mtm) outliers start: 46 outliers final: 26 residues processed: 191 average time/residue: 0.7774 time to fit residues: 159.8589 Evaluate side-chains 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 383 CYS Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 43 optimal weight: 0.4980 chunk 98 optimal weight: 0.0070 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.160002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121855 restraints weight = 13602.137| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.22 r_work: 0.3116 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15021 Z= 0.113 Angle : 0.575 6.764 20366 Z= 0.288 Chirality : 0.042 0.179 2346 Planarity : 0.004 0.036 2532 Dihedral : 15.783 158.941 2318 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.39 % Allowed : 21.45 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.50 (0.20), residues: 1830 helix: 0.85 (0.19), residues: 864 sheet: 2.93 (0.31), residues: 270 loop : -1.46 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.005 0.001 TYR B 253 PHE 0.010 0.001 PHE D 187 HIS 0.002 0.001 HIS E 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.11 (15017) covalent geometry : angle 0.57485 / 0.29 (20366) hydrogen bonds : bond 0.04043 / 2.74 ( 611) hydrogen bonds : angle 3.89571 / 2.69 ( 1710) Misc. bond : bond 0.00067 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.5205 (mmp) REVERT: C 293 ARG cc_start: 0.6787 (mpt180) cc_final: 0.6188 (tmm160) REVERT: D 115 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7959 (ttt90) REVERT: E 116 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7172 (ptpp) REVERT: E 138 ARG cc_start: 0.7756 (ttp-110) cc_final: 0.7532 (ttt180) REVERT: F 93 MET cc_start: 0.5329 (mpt) cc_final: 0.4519 (mtm) REVERT: F 115 ARG cc_start: 0.7584 (ttt-90) cc_final: 0.7148 (ttt-90) REVERT: F 122 LYS cc_start: 0.5309 (OUTLIER) cc_final: 0.4562 (ttmt) REVERT: F 216 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8020 (tt) REVERT: F 364 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6856 (ptpp) REVERT: A 93 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.3987 (tmt) REVERT: A 116 LYS cc_start: 0.5467 (ttpt) cc_final: 0.5167 (ptpt) REVERT: A 204 ILE cc_start: 0.6022 (OUTLIER) cc_final: 0.5725 (mp) REVERT: A 241 ASP cc_start: 0.5886 (m-30) cc_final: 0.5544 (m-30) REVERT: B 115 ARG cc_start: 0.7022 (tmm-80) cc_final: 0.6676 (ttt-90) REVERT: B 176 GLU cc_start: 0.7732 (tt0) cc_final: 0.7216 (tp30) outliers start: 36 outliers final: 16 residues processed: 193 average time/residue: 0.7991 time to fit residues: 165.3643 Evaluate side-chains 181 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 288 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.154878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114308 restraints weight = 13286.650| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.30 r_work: 0.3024 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15021 Z= 0.160 Angle : 0.655 8.204 20366 Z= 0.336 Chirality : 0.045 0.232 2346 Planarity : 0.004 0.039 2532 Dihedral : 15.920 159.189 2310 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.12 % Allowed : 22.11 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1830 helix: 0.78 (0.19), residues: 858 sheet: 2.87 (0.31), residues: 270 loop : -1.48 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.008 0.001 TYR C 253 PHE 0.010 0.001 PHE B 184 HIS 0.003 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (15017) covalent geometry : angle 0.65462 / 0.34 (20366) hydrogen bonds : bond 0.06060 / 4.08 ( 611) hydrogen bonds : angle 4.14519 / 2.86 ( 1710) Misc. bond : bond 0.00110 / 0.06 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: C 93 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5302 (mmp) REVERT: C 293 ARG cc_start: 0.7042 (mpt180) cc_final: 0.6447 (tmm160) REVERT: D 124 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5631 (mm) REVERT: D 216 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8653 (tt) REVERT: E 116 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7220 (ptpp) REVERT: E 138 ARG cc_start: 0.7719 (ttp-110) cc_final: 0.7478 (ttt180) REVERT: F 93 MET cc_start: 0.5353 (mpt) cc_final: 0.4509 (mtm) REVERT: F 115 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.7224 (ttt-90) REVERT: F 122 LYS cc_start: 0.5294 (OUTLIER) cc_final: 0.4568 (ttmt) REVERT: F 364 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6884 (ptpp) REVERT: A 93 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4026 (tmt) REVERT: A 204 ILE cc_start: 0.6042 (OUTLIER) cc_final: 0.5751 (mp) REVERT: A 241 ASP cc_start: 0.5930 (m-30) cc_final: 0.5614 (m-30) REVERT: B 115 ARG cc_start: 0.7088 (tmm-80) cc_final: 0.6734 (ttt-90) REVERT: B 165 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7442 (mmpt) outliers start: 32 outliers final: 20 residues processed: 183 average time/residue: 0.7355 time to fit residues: 144.6731 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 234 GLN Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 383 CYS Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 69 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 166 ASN E 267 GLN F 166 ASN A 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.156299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116375 restraints weight = 13338.938| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.29 r_work: 0.3061 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15021 Z= 0.143 Angle : 0.627 8.581 20366 Z= 0.320 Chirality : 0.044 0.212 2346 Planarity : 0.004 0.039 2532 Dihedral : 15.907 159.477 2310 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.79 % Allowed : 22.58 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 0.42 (0.20), residues: 1830 helix: 0.77 (0.19), residues: 864 sheet: 2.89 (0.31), residues: 270 loop : -1.46 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 115 TYR 0.007 0.001 TYR D 217 PHE 0.010 0.001 PHE B 184 HIS 0.003 0.001 HIS C 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (15017) covalent geometry : angle 0.62659 / 0.32 (20366) hydrogen bonds : bond 0.05473 / 3.70 ( 611) hydrogen bonds : angle 4.08993 / 2.82 ( 1710) Misc. bond : bond 0.00096 / 0.05 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6831.54 seconds wall clock time: 116 minutes 24.83 seconds (6984.83 seconds total)