Starting phenix.real_space_refine on Wed Apr 8 05:12:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tu5_26126/04_2026/7tu5_26126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tu5_26126/04_2026/7tu5_26126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tu5_26126/04_2026/7tu5_26126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tu5_26126/04_2026/7tu5_26126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tu5_26126/04_2026/7tu5_26126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tu5_26126/04_2026/7tu5_26126.map" } resolution = 2.1 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= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19206 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 42 5.16 5 C 12624 2.51 5 N 3396 2.21 5 O 3588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3274 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 416} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 126 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 3.10, per 1000 atoms: 0.16 Number of scatterers: 19656 At special positions: 0 Unit cell: (125.97, 133.722, 98.838, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 Mg 6 11.99 O 3588 8.00 N 3396 7.00 C 12624 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=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 769.1 milliseconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 75.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 64 through 91 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG A 142 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 145 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 147 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS A 208 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR A 247 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 298 through 325 Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 411 through 425 Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.769A pdb=" N TYR B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 64 through 91 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.631A pdb=" N PHE B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG B 142 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B 145 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 147 " --> pdb=" O LYS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS B 208 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR B 247 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 298 through 325 Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 389 removed outlier: 3.715A pdb=" N GLU B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 411 through 425 Processing helix chain 'B' and resid 427 through 439 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 47 through 50 Processing helix chain 'C' and resid 64 through 91 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG C 142 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 145 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 147 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS C 208 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 228 Processing helix chain 'C' and resid 243 through 268 removed outlier: 3.761A pdb=" N TYR C 247 " --> pdb=" O HIS C 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP C 261 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU C 283 " --> pdb=" O TYR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 298 through 325 Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 439 Processing helix chain 'D' and resid 4 through 8 Processing helix chain 'D' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 64 through 91 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG D 142 " --> pdb=" O TYR D 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP D 145 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 147 " --> pdb=" O LYS D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.687A pdb=" N LYS D 208 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 228 Processing helix chain 'D' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR D 247 " --> pdb=" O HIS D 243 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 248 " --> pdb=" O PRO D 244 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 261 " --> pdb=" O TYR D 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU D 283 " --> pdb=" O TYR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 298 through 325 Processing helix chain 'D' and resid 325 through 332 Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 344 through 359 Processing helix chain 'D' and resid 362 through 389 removed outlier: 3.715A pdb=" N GLU D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 411 through 425 Processing helix chain 'D' and resid 427 through 439 Processing helix chain 'E' and resid 4 through 8 Processing helix chain 'E' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 64 through 91 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E 135 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.650A pdb=" N ARG E 142 " --> pdb=" O TYR E 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP E 145 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 147 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.516A pdb=" N ASN E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 204 through 208 removed outlier: 3.686A pdb=" N LYS E 208 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 228 Processing helix chain 'E' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR E 247 " --> pdb=" O HIS E 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP E 261 " --> pdb=" O TYR E 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 285 removed outlier: 4.192A pdb=" N ALA E 276 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 298 through 325 Processing helix chain 'E' and resid 325 through 332 Processing helix chain 'E' and resid 338 through 342 Processing helix chain 'E' and resid 344 through 359 Processing helix chain 'E' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 403 Processing helix chain 'E' and resid 411 through 425 Processing helix chain 'E' and resid 427 through 439 Processing helix chain 'F' and resid 4 through 8 Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.770A pdb=" N TYR F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 64 through 91 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 101 through 115 removed outlier: 3.632A pdb=" N PHE F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.606A pdb=" N GLU F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 removed outlier: 3.649A pdb=" N ARG F 142 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP F 145 " --> pdb=" O ARG F 142 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU F 147 " --> pdb=" O LYS F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.515A pdb=" N ASN F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 204 through 208 removed outlier: 3.687A pdb=" N LYS F 208 " --> pdb=" O ILE F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 228 Processing helix chain 'F' and resid 243 through 268 removed outlier: 3.760A pdb=" N TYR F 247 " --> pdb=" O HIS F 243 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU F 248 " --> pdb=" O PRO F 244 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP F 261 " --> pdb=" O TYR F 257 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 262 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 285 removed outlier: 4.191A pdb=" N ALA F 276 " --> pdb=" O PRO F 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS F 282 " --> pdb=" O GLU F 278 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU F 283 " --> pdb=" O TYR F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 298 through 325 Processing helix chain 'F' and resid 325 through 332 Processing helix chain 'F' and resid 338 through 342 Processing helix chain 'F' and resid 344 through 359 Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.714A pdb=" N GLU F 374 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 403 Processing helix chain 'F' and resid 411 through 425 Processing helix chain 'F' and resid 427 through 439 1237 hydrogen bonds defined for protein. 3567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3192 1.29 - 1.42: 5292 1.42 - 1.55: 11459 1.55 - 1.68: 19 1.68 - 1.81: 66 Bond restraints: 20028 Sorted by residual: bond pdb=" C ARG B 77 " pdb=" O ARG B 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.29e+01 bond pdb=" C ARG E 77 " pdb=" O ARG E 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.28e+01 bond pdb=" C ARG C 77 " pdb=" O ARG C 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.27e+01 bond pdb=" C ARG F 77 " pdb=" O ARG F 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.26e+01 bond pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.26e-02 6.30e+03 3.26e+01 ... (remaining 20023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 25814 1.85 - 3.71: 975 3.71 - 5.56: 279 5.56 - 7.42: 34 7.42 - 9.27: 6 Bond angle restraints: 27108 Sorted by residual: angle pdb=" N HIS E 63 " pdb=" CA HIS E 63 " pdb=" C HIS E 63 " ideal model delta sigma weight residual 110.10 119.37 -9.27 1.49e+00 4.50e-01 3.87e+01 angle pdb=" N HIS A 63 " pdb=" CA HIS A 63 " pdb=" C HIS A 63 " ideal model delta sigma weight residual 110.10 119.35 -9.25 1.49e+00 4.50e-01 3.85e+01 angle pdb=" N HIS C 63 " pdb=" CA HIS C 63 " pdb=" C HIS C 63 " ideal model delta sigma weight residual 110.10 119.33 -9.23 1.49e+00 4.50e-01 3.84e+01 angle pdb=" N HIS B 63 " pdb=" CA HIS B 63 " pdb=" C HIS B 63 " ideal model delta sigma weight residual 110.10 119.33 -9.23 1.49e+00 4.50e-01 3.84e+01 angle pdb=" N HIS D 63 " pdb=" CA HIS D 63 " pdb=" C HIS D 63 " ideal model delta sigma weight residual 110.10 119.32 -9.22 1.49e+00 4.50e-01 3.83e+01 ... (remaining 27103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 10464 17.18 - 34.36: 1086 34.36 - 51.55: 288 51.55 - 68.73: 78 68.73 - 85.91: 24 Dihedral angle restraints: 11940 sinusoidal: 4446 harmonic: 7494 Sorted by residual: dihedral pdb=" C ILE F 260 " pdb=" N ILE F 260 " pdb=" CA ILE F 260 " pdb=" CB ILE F 260 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ILE B 260 " pdb=" N ILE B 260 " pdb=" CA ILE B 260 " pdb=" CB ILE B 260 " ideal model delta harmonic sigma weight residual -122.00 -134.51 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C ILE A 260 " pdb=" N ILE A 260 " pdb=" CA ILE A 260 " pdb=" CB ILE A 260 " ideal model delta harmonic sigma weight residual -122.00 -134.50 12.50 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 11937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2824 0.091 - 0.183: 181 0.183 - 0.274: 31 0.274 - 0.366: 26 0.366 - 0.457: 16 Chirality restraints: 3078 Sorted by residual: chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA ILE F 260 " pdb=" N ILE F 260 " pdb=" C ILE F 260 " pdb=" CB ILE F 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CA ILE A 260 " pdb=" N ILE A 260 " pdb=" C ILE A 260 " pdb=" CB ILE A 260 " both_signs ideal model delta sigma weight residual False 2.43 1.98 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 3075 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 259 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ILE F 259 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE F 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE F 260 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 259 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C ILE D 259 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE D 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE D 260 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 259 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C ILE B 259 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE B 259 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE B 260 " -0.017 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 54 2.51 - 3.11: 14099 3.11 - 3.70: 30873 3.70 - 4.30: 45208 4.30 - 4.90: 76609 Nonbonded interactions: 166843 Sorted by model distance: nonbonded pdb=" NE2 HIS C 116 " pdb="MG MG C 601 " model vdw 1.910 2.250 nonbonded pdb=" NE2 HIS B 116 " pdb="MG MG B 601 " model vdw 1.910 2.250 nonbonded pdb=" NE2 HIS D 116 " pdb="MG MG D 601 " model vdw 1.911 2.250 nonbonded pdb=" NE2 HIS E 116 " pdb="MG MG E 601 " model vdw 1.911 2.250 nonbonded pdb=" NE2 HIS A 116 " pdb="MG MG A 601 " model vdw 1.911 2.250 ... (remaining 166838 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: 0.06 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: 5.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.260 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.009 0.072 20028 Z= 0.624 Angle : 0.846 9.271 27108 Z= 0.543 Chirality : 0.064 0.457 3078 Planarity : 0.005 0.049 3456 Dihedral : 15.879 85.912 7140 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.54 % Allowed : 15.43 % Favored : 83.02 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 0.64 (0.17), residues: 2538 helix: 0.86 (0.13), residues: 1662 sheet: None (None), residues: 0 loop : -0.26 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 77 TYR 0.021 0.002 TYR E 305 PHE 0.022 0.001 PHE D 158 TRP 0.006 0.001 TRP F 240 HIS 0.009 0.001 HIS F 63 Details of bonding type rmsd covalent geometry : bond 0.00927 (20028) covalent geometry : angle 0.84565 (27108) hydrogen bonds : bond 0.15063 ( 1237) hydrogen bonds : angle 4.99010 ( 3567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 582 time to evaluate : 0.551 Fit side-chains REVERT: B 220 PHE cc_start: 0.7959 (t80) cc_final: 0.7728 (t80) REVERT: C 261 ASP cc_start: 0.7070 (m-30) cc_final: 0.6648 (m-30) REVERT: D 261 ASP cc_start: 0.6989 (m-30) cc_final: 0.6678 (m-30) REVERT: E 261 ASP cc_start: 0.7121 (m-30) cc_final: 0.6686 (m-30) outliers start: 30 outliers final: 7 residues processed: 589 average time/residue: 0.7063 time to fit residues: 459.9680 Evaluate side-chains 539 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 532 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 161 ASN B 153 GLN C 393 HIS D 3 ASN D 153 GLN D 343 ASN E 3 ASN E 161 ASN F 3 ASN F 343 ASN F 347 GLN F 393 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.131100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118279 restraints weight = 22518.737| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.16 r_work: 0.3540 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20028 Z= 0.125 Angle : 0.448 4.823 27108 Z= 0.246 Chirality : 0.035 0.151 3078 Planarity : 0.004 0.037 3456 Dihedral : 4.169 54.269 2831 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.03 % Allowed : 16.87 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.67 (0.17), residues: 2538 helix: 1.69 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.13 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 433 TYR 0.018 0.001 TYR B 305 PHE 0.014 0.001 PHE F 220 TRP 0.004 0.001 TRP D 240 HIS 0.005 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00281 (20028) covalent geometry : angle 0.44820 (27108) hydrogen bonds : bond 0.04675 ( 1237) hydrogen bonds : angle 3.67975 ( 3567) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 549 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.8586 (mmt) cc_final: 0.8276 (mmt) REVERT: B 373 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7952 (t80) outliers start: 59 outliers final: 19 residues processed: 578 average time/residue: 0.7206 time to fit residues: 458.6107 Evaluate side-chains 551 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 531 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 400 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 389 ASN A 395 ASN B 161 ASN B 267 ASN B 395 ASN C 153 GLN C 389 ASN C 393 HIS C 395 ASN D 3 ASN D 161 ASN D 343 ASN E 3 ASN E 161 ASN E 395 ASN F 170 GLN F 343 ASN F 395 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.127397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.114304 restraints weight = 22389.850| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.15 r_work: 0.3477 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20028 Z= 0.247 Angle : 0.543 5.706 27108 Z= 0.291 Chirality : 0.042 0.149 3078 Planarity : 0.004 0.039 3456 Dihedral : 4.016 34.152 2820 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.83 % Allowed : 17.34 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.33 (0.16), residues: 2538 helix: 1.46 (0.12), residues: 1638 sheet: None (None), residues: 0 loop : -0.07 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 433 TYR 0.018 0.002 TYR B 305 PHE 0.021 0.002 PHE F 220 TRP 0.007 0.002 TRP D 240 HIS 0.007 0.002 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00604 (20028) covalent geometry : angle 0.54297 (27108) hydrogen bonds : bond 0.05919 ( 1237) hydrogen bonds : angle 3.82554 ( 3567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 557 time to evaluate : 0.768 Fit side-chains REVERT: C 136 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8187 (tttm) REVERT: D 136 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8355 (tttm) outliers start: 55 outliers final: 25 residues processed: 585 average time/residue: 0.7151 time to fit residues: 462.1848 Evaluate side-chains 575 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 548 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 219 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 389 ASN C 3 ASN D 3 ASN D 161 ASN D 343 ASN E 3 ASN E 161 ASN F 6 HIS F 176 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.128190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115044 restraints weight = 22291.713| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.16 r_work: 0.3486 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20028 Z= 0.186 Angle : 0.489 5.590 27108 Z= 0.265 Chirality : 0.038 0.140 3078 Planarity : 0.004 0.037 3456 Dihedral : 3.830 23.335 2816 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.98 % Allowed : 18.31 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.37 (0.16), residues: 2538 helix: 1.49 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.08 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 433 TYR 0.013 0.002 TYR C 325 PHE 0.019 0.002 PHE C 220 TRP 0.007 0.001 TRP D 240 HIS 0.005 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00447 (20028) covalent geometry : angle 0.48941 (27108) hydrogen bonds : bond 0.05355 ( 1237) hydrogen bonds : angle 3.75404 ( 3567) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 565 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8157 (tttm) REVERT: D 136 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8318 (tttm) REVERT: E 150 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8295 (mtpt) outliers start: 58 outliers final: 35 residues processed: 595 average time/residue: 0.7001 time to fit residues: 460.7540 Evaluate side-chains 584 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 546 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 400 GLN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 203 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 389 ASN B 267 ASN C 120 ASN C 345 GLN D 3 ASN D 153 GLN D 161 ASN D 176 GLN D 343 ASN E 3 ASN E 161 ASN F 3 ASN F 6 HIS F 176 GLN F 343 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.117167 restraints weight = 22430.262| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.16 r_work: 0.3522 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20028 Z= 0.115 Angle : 0.431 5.470 27108 Z= 0.235 Chirality : 0.034 0.132 3078 Planarity : 0.004 0.035 3456 Dihedral : 3.584 21.787 2816 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.57 % Allowed : 19.44 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.68 (0.16), residues: 2538 helix: 1.75 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.02 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 433 TYR 0.011 0.001 TYR D 279 PHE 0.016 0.001 PHE C 220 TRP 0.007 0.001 TRP D 240 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00258 (20028) covalent geometry : angle 0.43122 (27108) hydrogen bonds : bond 0.04445 ( 1237) hydrogen bonds : angle 3.63664 ( 3567) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 570 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 340 ASP cc_start: 0.7382 (m-30) cc_final: 0.7131 (m-30) REVERT: C 334 PHE cc_start: 0.8420 (t80) cc_final: 0.8100 (t80) REVERT: E 150 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8186 (mtpt) outliers start: 50 outliers final: 30 residues processed: 597 average time/residue: 0.6975 time to fit residues: 460.8458 Evaluate side-chains 587 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 556 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 257 TYR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 66 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 185 optimal weight: 0.3980 chunk 220 optimal weight: 0.0060 chunk 170 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 176 GLN A 343 ASN A 389 ASN B 161 ASN C 267 ASN C 415 ASN D 3 ASN D 153 GLN D 161 ASN D 343 ASN E 3 ASN E 153 GLN E 161 ASN E 170 GLN F 3 ASN F 176 GLN F 267 ASN F 343 ASN F 353 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116712 restraints weight = 22364.331| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.15 r_work: 0.3513 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20028 Z= 0.128 Angle : 0.448 6.424 27108 Z= 0.242 Chirality : 0.035 0.151 3078 Planarity : 0.004 0.038 3456 Dihedral : 3.536 20.761 2814 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.09 % Allowed : 19.08 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.68 (0.16), residues: 2538 helix: 1.76 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : 0.01 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 433 TYR 0.010 0.001 TYR C 293 PHE 0.017 0.001 PHE C 220 TRP 0.006 0.001 TRP C 240 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00297 (20028) covalent geometry : angle 0.44762 (27108) hydrogen bonds : bond 0.04628 ( 1237) hydrogen bonds : angle 3.65246 ( 3567) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 552 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8164 (tttm) REVERT: D 142 ARG cc_start: 0.8061 (ptm-80) cc_final: 0.7860 (ptm-80) REVERT: E 150 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8172 (mtpt) outliers start: 60 outliers final: 38 residues processed: 583 average time/residue: 0.7095 time to fit residues: 457.1622 Evaluate side-chains 588 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 548 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 250 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 247 optimal weight: 0.0060 chunk 19 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 343 ASN A 389 ASN B 161 ASN C 161 ASN C 345 GLN D 3 ASN D 153 GLN D 161 ASN D 343 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN F 176 GLN F 343 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115994 restraints weight = 22377.505| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.15 r_work: 0.3503 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20028 Z= 0.149 Angle : 0.471 6.780 27108 Z= 0.254 Chirality : 0.036 0.142 3078 Planarity : 0.004 0.039 3456 Dihedral : 3.608 20.681 2814 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.78 % Allowed : 20.01 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.60 (0.16), residues: 2538 helix: 1.71 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.05 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 433 TYR 0.009 0.001 TYR D 210 PHE 0.018 0.001 PHE C 220 TRP 0.006 0.001 TRP D 240 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00352 (20028) covalent geometry : angle 0.47084 (27108) hydrogen bonds : bond 0.04899 ( 1237) hydrogen bonds : angle 3.69234 ( 3567) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 554 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8179 (tttm) REVERT: C 334 PHE cc_start: 0.8424 (t80) cc_final: 0.8135 (t80) REVERT: D 142 ARG cc_start: 0.8068 (ptm-80) cc_final: 0.7864 (ptm-80) REVERT: E 150 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8240 (mtpt) outliers start: 54 outliers final: 34 residues processed: 581 average time/residue: 0.7056 time to fit residues: 453.9600 Evaluate side-chains 592 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 556 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 368 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 37 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 246 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 343 ASN A 389 ASN B 153 GLN B 161 ASN C 345 GLN D 3 ASN D 153 GLN D 161 ASN D 343 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.115407 restraints weight = 22243.904| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.14 r_work: 0.3494 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20028 Z= 0.174 Angle : 0.498 7.902 27108 Z= 0.268 Chirality : 0.038 0.163 3078 Planarity : 0.004 0.041 3456 Dihedral : 3.689 20.734 2814 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.57 % Allowed : 20.11 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.52 (0.16), residues: 2538 helix: 1.63 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.06 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 433 TYR 0.012 0.001 TYR C 293 PHE 0.020 0.001 PHE F 220 TRP 0.006 0.001 TRP D 240 HIS 0.005 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00418 (20028) covalent geometry : angle 0.49757 (27108) hydrogen bonds : bond 0.05195 ( 1237) hydrogen bonds : angle 3.74168 ( 3567) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 555 time to evaluate : 0.623 Fit side-chains REVERT: C 136 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8198 (tttm) REVERT: D 142 ARG cc_start: 0.8069 (ptm-80) cc_final: 0.7852 (ptm-80) REVERT: E 150 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8249 (mtpt) REVERT: E 176 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7919 (mp-120) outliers start: 50 outliers final: 34 residues processed: 579 average time/residue: 0.7072 time to fit residues: 452.0282 Evaluate side-chains 592 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 555 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 246 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 389 ASN B 161 ASN C 345 GLN D 3 ASN D 153 GLN D 161 ASN D 343 ASN E 3 ASN E 161 ASN E 170 GLN E 176 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.129049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116140 restraints weight = 22341.229| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.14 r_work: 0.3506 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20028 Z= 0.145 Angle : 0.482 7.567 27108 Z= 0.261 Chirality : 0.036 0.169 3078 Planarity : 0.004 0.041 3456 Dihedral : 3.625 20.502 2814 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.47 % Allowed : 20.63 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.58 (0.16), residues: 2538 helix: 1.68 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.04 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 433 TYR 0.013 0.001 TYR D 279 PHE 0.019 0.001 PHE F 220 TRP 0.006 0.001 TRP C 240 HIS 0.004 0.001 HIS F 116 Details of bonding type rmsd covalent geometry : bond 0.00340 (20028) covalent geometry : angle 0.48186 (27108) hydrogen bonds : bond 0.04869 ( 1237) hydrogen bonds : angle 3.71870 ( 3567) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 555 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8179 (tttm) REVERT: C 334 PHE cc_start: 0.8427 (t80) cc_final: 0.8141 (t80) REVERT: D 142 ARG cc_start: 0.8063 (ptm-80) cc_final: 0.7843 (ptm-80) REVERT: D 336 GLN cc_start: 0.8496 (mt0) cc_final: 0.8272 (mt0) REVERT: E 150 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8245 (mtpt) REVERT: E 176 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8011 (mp-120) outliers start: 48 outliers final: 34 residues processed: 578 average time/residue: 0.7009 time to fit residues: 448.2147 Evaluate side-chains 588 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 551 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 136 LYS Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 0.0170 chunk 178 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 203 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN B 161 ASN C 345 GLN D 3 ASN D 153 GLN D 161 ASN D 343 ASN E 3 ASN E 161 ASN E 170 GLN E 345 GLN F 267 ASN F 343 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117097 restraints weight = 22464.707| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.15 r_work: 0.3521 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20028 Z= 0.121 Angle : 0.467 8.108 27108 Z= 0.253 Chirality : 0.035 0.173 3078 Planarity : 0.004 0.041 3456 Dihedral : 3.534 20.763 2814 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.38 % Favored : 98.58 % Rotamer: Outliers : 1.80 % Allowed : 21.14 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.68 (0.16), residues: 2538 helix: 1.76 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.01 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 433 TYR 0.015 0.001 TYR D 279 PHE 0.017 0.001 PHE F 220 TRP 0.006 0.001 TRP C 240 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00276 (20028) covalent geometry : angle 0.46733 (27108) hydrogen bonds : bond 0.04519 ( 1237) hydrogen bonds : angle 3.68732 ( 3567) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 566 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: C 136 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8167 (tttm) REVERT: C 334 PHE cc_start: 0.8418 (t80) cc_final: 0.8129 (t80) REVERT: D 336 GLN cc_start: 0.8462 (mt0) cc_final: 0.8242 (mt0) REVERT: E 150 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8205 (mtpt) REVERT: F 326 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7319 (tm-30) outliers start: 35 outliers final: 31 residues processed: 585 average time/residue: 0.6849 time to fit residues: 443.3690 Evaluate side-chains 552 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 519 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 215 SER Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 304 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 129 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 226 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 389 ASN B 267 ASN C 161 ASN D 153 GLN D 161 ASN D 343 ASN E 3 ASN E 161 ASN E 176 GLN F 267 ASN F 343 ASN F 347 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117017 restraints weight = 22456.143| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.14 r_work: 0.3519 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20028 Z= 0.127 Angle : 0.477 8.254 27108 Z= 0.256 Chirality : 0.035 0.174 3078 Planarity : 0.004 0.042 3456 Dihedral : 3.508 19.955 2814 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.38 % Favored : 98.58 % Rotamer: Outliers : 2.01 % Allowed : 21.04 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % 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: 1.67 (0.16), residues: 2538 helix: 1.76 (0.13), residues: 1638 sheet: None (None), residues: 0 loop : -0.03 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 433 TYR 0.011 0.001 TYR F 325 PHE 0.016 0.001 PHE D 220 TRP 0.007 0.001 TRP F 240 HIS 0.004 0.001 HIS F 116 Details of bonding type rmsd covalent geometry : bond 0.00292 (20028) covalent geometry : angle 0.47707 (27108) hydrogen bonds : bond 0.04573 ( 1237) hydrogen bonds : angle 3.68634 ( 3567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10362.40 seconds wall clock time: 175 minutes 50.70 seconds (10550.70 seconds total)