Starting phenix.real_space_refine on Wed Mar 4 16:09:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u96_20694/03_2026/6u96_20694.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u96_20694/03_2026/6u96_20694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u96_20694/03_2026/6u96_20694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u96_20694/03_2026/6u96_20694.map" model { file = "/net/cci-nas-00/data/ceres_data/6u96_20694/03_2026/6u96_20694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u96_20694/03_2026/6u96_20694.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 110 5.16 5 C 9410 2.51 5 N 2510 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'EEP:plan-1': 1, 'ALO:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.71, per 1000 atoms: 0.18 Number of scatterers: 14910 At special positions: 0 Unit cell: (87.74, 102.72, 204.37, 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 110 16.00 P 10 15.00 O 2870 8.00 N 2510 7.00 C 9410 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 586.6 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 25 sheets defined 42.8% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.568A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.630A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 114 through 125 removed outlier: 4.212A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.652A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 4.172A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.725A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.989A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.550A pdb=" N MET A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 4.009A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.977A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.947A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 306' Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.576A pdb=" N MET A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 317 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.566A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 removed outlier: 3.735A pdb=" N TYR A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.567A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.631A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 114 through 125 removed outlier: 4.213A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.653A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.173A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.724A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.988A pdb=" N ILE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.551A pdb=" N MET B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 4.009A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.977A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.947A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.576A pdb=" N MET B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 317 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 removed outlier: 3.566A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.735A pdb=" N TYR B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.567A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.630A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 114 through 125 removed outlier: 4.212A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.653A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 4.173A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.725A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.989A pdb=" N ILE C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.550A pdb=" N MET C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 4.010A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.976A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.947A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 302 through 306' Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.576A pdb=" N MET C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 317 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.566A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 365 removed outlier: 3.735A pdb=" N TYR C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.567A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.630A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 114 through 125 removed outlier: 4.212A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.653A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 4.174A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.725A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 206 through 216 removed outlier: 3.989A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.550A pdb=" N MET D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 removed outlier: 4.009A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.976A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.947A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 302 through 306' Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.576A pdb=" N MET D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.566A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 365 removed outlier: 3.735A pdb=" N TYR D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.568A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.630A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR E 91 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 114 through 125 removed outlier: 4.212A pdb=" N MET E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE E 122 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.653A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 4.173A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.725A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 206 through 216 removed outlier: 3.988A pdb=" N ILE E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.551A pdb=" N MET E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 4.009A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.977A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.946A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.577A pdb=" N MET E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE E 317 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR E 318 " --> pdb=" O GLN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.567A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 365 removed outlier: 3.736A pdb=" N TYR E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.563A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42 removed outlier: 4.421A pdb=" N GLN A 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 removed outlier: 4.424A pdb=" N GLN E 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12 removed outlier: 3.564A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.533A pdb=" N GLN C 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB3, first strand: chain 'C' and resid 8 through 12 removed outlier: 3.562A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AB6, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'D' and resid 8 through 12 removed outlier: 3.563A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 8 through 12 removed outlier: 3.562A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AC6, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.692A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 316 hydrogen bonds defined for protein. 858 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: 1.67 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2486 1.31 - 1.44: 3934 1.44 - 1.57: 8615 1.57 - 1.70: 20 1.70 - 1.83: 190 Bond restraints: 15245 Sorted by residual: bond pdb=" C CYS H 4 " pdb=" N HYP H 5 " ideal model delta sigma weight residual 1.329 1.488 -0.159 1.40e-02 5.10e+03 1.28e+02 bond pdb=" C CYS J 4 " pdb=" N HYP J 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS G 4 " pdb=" N HYP G 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS I 4 " pdb=" N HYP I 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS F 4 " pdb=" N HYP F 5 " ideal model delta sigma weight residual 1.329 1.486 -0.157 1.40e-02 5.10e+03 1.26e+02 ... (remaining 15240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 19847 2.49 - 4.98: 715 4.98 - 7.46: 113 7.46 - 9.95: 15 9.95 - 12.44: 15 Bond angle restraints: 20705 Sorted by residual: angle pdb=" CD1 TRP F 7 " pdb=" NE1 TRP F 7 " pdb=" CE2 TRP F 7 " ideal model delta sigma weight residual 108.90 120.67 -11.77 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP H 7 " pdb=" NE1 TRP H 7 " pdb=" CE2 TRP H 7 " ideal model delta sigma weight residual 108.90 120.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP J 7 " pdb=" NE1 TRP J 7 " pdb=" CE2 TRP J 7 " ideal model delta sigma weight residual 108.90 120.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP I 7 " pdb=" NE1 TRP I 7 " pdb=" CE2 TRP I 7 " ideal model delta sigma weight residual 108.90 120.65 -11.75 1.80e+00 3.09e-01 4.26e+01 angle pdb=" CD1 TRP G 7 " pdb=" NE1 TRP G 7 " pdb=" CE2 TRP G 7 " ideal model delta sigma weight residual 108.90 120.62 -11.72 1.80e+00 3.09e-01 4.24e+01 ... (remaining 20700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 8975 24.43 - 48.87: 190 48.87 - 73.30: 15 73.30 - 97.74: 10 97.74 - 122.17: 5 Dihedral angle restraints: 9195 sinusoidal: 3735 harmonic: 5460 Sorted by residual: dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 177.82 122.17 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 177.83 122.17 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 177.85 122.15 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 9192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2258 0.157 - 0.313: 42 0.313 - 0.470: 0 0.470 - 0.626: 0 0.626 - 0.783: 5 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA HIC E 73 " pdb=" N HIC E 73 " pdb=" C HIC E 73 " pdb=" CB HIC E 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA HIC D 73 " pdb=" N HIC D 73 " pdb=" C HIC D 73 " pdb=" CB HIC D 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA HIC A 73 " pdb=" N HIC A 73 " pdb=" C HIC A 73 " pdb=" CB HIC A 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 ... (remaining 2302 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 69 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 69 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO E 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 70 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 69 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 70 " -0.036 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 40 2.45 - 3.06: 8363 3.06 - 3.68: 19943 3.68 - 4.29: 27494 4.29 - 4.90: 46955 Nonbonded interactions: 102795 Sorted by model distance: nonbonded pdb=" SG CYS I 4 " pdb=" CD1 TRP I 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS J 4 " pdb=" CD1 TRP J 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS G 4 " pdb=" CD1 TRP G 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS H 4 " pdb=" CD1 TRP H 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS F 4 " pdb=" CD1 TRP F 7 " model vdw 1.838 3.620 ... (remaining 102790 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 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 : 0.014 0.219 15250 Z= 0.747 Angle : 1.120 12.440 20705 Z= 0.579 Chirality : 0.071 0.783 2305 Planarity : 0.007 0.064 2630 Dihedral : 11.419 122.172 5695 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.63 % Allowed : 4.13 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.97 (0.15), residues: 1830 helix: -4.52 (0.09), residues: 580 sheet: -1.96 (0.26), residues: 385 loop : -2.97 (0.17), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 372 TYR 0.024 0.002 TYR D 294 PHE 0.016 0.003 PHE B 262 TRP 0.027 0.003 TRP C 340 HIS 0.004 0.002 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.01379 (15245) covalent geometry : angle 1.12018 (20705) hydrogen bonds : bond 0.37798 ( 316) hydrogen bonds : angle 9.04257 ( 858) Misc. bond : bond 0.05523 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 230 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 358 THR cc_start: 0.9112 (p) cc_final: 0.8888 (t) REVERT: E 216 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8528 (pp) outliers start: 10 outliers final: 4 residues processed: 240 average time/residue: 0.1279 time to fit residues: 44.3243 Evaluate side-chains 121 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 121 GLN B 137 GLN B 371 HIS C 137 GLN D 360 GLN D 371 HIS E 121 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.051176 restraints weight = 46241.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.052819 restraints weight = 24215.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.053945 restraints weight = 15450.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.054660 restraints weight = 11180.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.055230 restraints weight = 8940.219| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15250 Z= 0.231 Angle : 0.777 6.900 20705 Z= 0.381 Chirality : 0.052 0.204 2305 Planarity : 0.005 0.054 2630 Dihedral : 10.149 112.408 2210 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.33 % Allowed : 7.56 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.17), residues: 1830 helix: -3.16 (0.16), residues: 590 sheet: -1.79 (0.27), residues: 385 loop : -2.45 (0.18), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 372 TYR 0.015 0.001 TYR E 294 PHE 0.010 0.001 PHE C 200 TRP 0.013 0.001 TRP B 340 HIS 0.004 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00552 (15245) covalent geometry : angle 0.77706 (20705) hydrogen bonds : bond 0.05899 ( 316) hydrogen bonds : angle 5.94324 ( 858) Misc. bond : bond 0.00192 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.7960 (t0) cc_final: 0.7587 (t0) REVERT: A 283 MET cc_start: 0.9057 (tpp) cc_final: 0.8699 (tpp) REVERT: A 325 MET cc_start: 0.8669 (mtt) cc_final: 0.8433 (mtt) REVERT: B 355 MET cc_start: 0.8468 (mmm) cc_final: 0.8044 (mtp) REVERT: E 283 MET cc_start: 0.8979 (tpp) cc_final: 0.8596 (tpp) outliers start: 21 outliers final: 10 residues processed: 151 average time/residue: 0.1194 time to fit residues: 27.1108 Evaluate side-chains 117 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.061677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.051671 restraints weight = 46910.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.053307 restraints weight = 24225.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.054474 restraints weight = 15351.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.055258 restraints weight = 11051.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.055792 restraints weight = 8736.257| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15250 Z= 0.155 Angle : 0.669 6.392 20705 Z= 0.319 Chirality : 0.048 0.161 2305 Planarity : 0.004 0.041 2630 Dihedral : 9.351 107.244 2210 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.54 % Allowed : 8.06 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.18), residues: 1830 helix: -2.23 (0.19), residues: 595 sheet: -1.60 (0.27), residues: 355 loop : -2.24 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.011 0.001 TYR C 294 PHE 0.007 0.001 PHE C 200 TRP 0.010 0.001 TRP B 340 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00365 (15245) covalent geometry : angle 0.66875 (20705) hydrogen bonds : bond 0.04760 ( 316) hydrogen bonds : angle 5.27393 ( 858) Misc. bond : bond 0.00008 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 208 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8902 (mt) REVERT: A 283 MET cc_start: 0.8962 (tpp) cc_final: 0.8626 (tpp) REVERT: B 205 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: B 208 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9127 (mt) REVERT: B 349 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8495 (mp) REVERT: B 355 MET cc_start: 0.8460 (mmm) cc_final: 0.8024 (mtp) REVERT: C 72 GLU cc_start: 0.7845 (tp30) cc_final: 0.7452 (tp30) REVERT: C 349 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8614 (mp) REVERT: D 82 MET cc_start: 0.8666 (mmm) cc_final: 0.8281 (tpt) REVERT: E 236 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8706 (pt) REVERT: E 283 MET cc_start: 0.8957 (tpp) cc_final: 0.8541 (tpp) outliers start: 40 outliers final: 15 residues processed: 153 average time/residue: 0.1012 time to fit residues: 24.7013 Evaluate side-chains 123 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.059975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.049966 restraints weight = 46863.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.051607 restraints weight = 24293.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.052737 restraints weight = 15386.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.053499 restraints weight = 11117.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.053999 restraints weight = 8836.375| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15250 Z= 0.202 Angle : 0.705 6.209 20705 Z= 0.337 Chirality : 0.050 0.163 2305 Planarity : 0.004 0.042 2630 Dihedral : 9.348 105.542 2210 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.29 % Allowed : 8.76 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.19), residues: 1830 helix: -1.89 (0.20), residues: 595 sheet: -1.71 (0.27), residues: 355 loop : -1.99 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 183 TYR 0.012 0.001 TYR A 294 PHE 0.015 0.001 PHE B 375 TRP 0.009 0.001 TRP D 340 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00486 (15245) covalent geometry : angle 0.70462 (20705) hydrogen bonds : bond 0.04936 ( 316) hydrogen bonds : angle 5.27011 ( 858) Misc. bond : bond 0.00008 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.520 Fit side-chains REVERT: A 208 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.9020 (mt) REVERT: A 283 MET cc_start: 0.8914 (tpp) cc_final: 0.8624 (tpp) REVERT: B 82 MET cc_start: 0.8790 (tpp) cc_final: 0.8588 (mmm) REVERT: B 283 MET cc_start: 0.8890 (tpp) cc_final: 0.8055 (mpp) REVERT: B 349 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8684 (mp) REVERT: B 355 MET cc_start: 0.8546 (mmm) cc_final: 0.8174 (mtp) REVERT: C 208 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9090 (mt) REVERT: C 349 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8746 (mp) REVERT: E 236 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8694 (pt) REVERT: E 283 MET cc_start: 0.8909 (tpp) cc_final: 0.8577 (tpp) REVERT: E 349 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8667 (mp) outliers start: 36 outliers final: 23 residues processed: 139 average time/residue: 0.1137 time to fit residues: 24.7831 Evaluate side-chains 129 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 0.0060 chunk 15 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.061335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.051260 restraints weight = 46450.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.052925 restraints weight = 24073.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.054072 restraints weight = 15262.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.054845 restraints weight = 11033.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.055380 restraints weight = 8774.574| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15250 Z= 0.121 Angle : 0.624 6.480 20705 Z= 0.294 Chirality : 0.047 0.166 2305 Planarity : 0.004 0.037 2630 Dihedral : 9.003 100.458 2210 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.22 % Allowed : 9.08 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.19), residues: 1830 helix: -1.51 (0.21), residues: 595 sheet: -1.65 (0.27), residues: 355 loop : -1.86 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.009 0.001 TYR B 294 PHE 0.009 0.001 PHE E 375 TRP 0.007 0.001 TRP D 340 HIS 0.002 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00284 (15245) covalent geometry : angle 0.62433 (20705) hydrogen bonds : bond 0.03729 ( 316) hydrogen bonds : angle 4.79569 ( 858) Misc. bond : bond 0.00011 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.590 Fit side-chains REVERT: A 124 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: A 283 MET cc_start: 0.8838 (tpp) cc_final: 0.8586 (tpp) REVERT: B 244 ASP cc_start: 0.7546 (t0) cc_final: 0.7270 (m-30) REVERT: B 269 MET cc_start: 0.8872 (ttm) cc_final: 0.8579 (ttm) REVERT: B 283 MET cc_start: 0.8867 (tpp) cc_final: 0.8015 (tpp) REVERT: B 304 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8948 (m) REVERT: B 349 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8764 (mp) REVERT: B 355 MET cc_start: 0.8536 (mmm) cc_final: 0.8077 (mtp) REVERT: C 49 GLN cc_start: 0.8684 (pp30) cc_final: 0.8411 (tm-30) REVERT: C 124 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8601 (m-10) REVERT: C 349 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8760 (mp) REVERT: D 82 MET cc_start: 0.8628 (mmm) cc_final: 0.8254 (tpt) REVERT: E 111 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7814 (p0) REVERT: E 236 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8714 (pt) REVERT: E 283 MET cc_start: 0.8867 (tpp) cc_final: 0.8628 (tpp) outliers start: 35 outliers final: 20 residues processed: 139 average time/residue: 0.1076 time to fit residues: 23.5619 Evaluate side-chains 129 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 0.0070 chunk 117 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 overall best weight: 6.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.060219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.050375 restraints weight = 46785.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.051959 restraints weight = 24869.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.053042 restraints weight = 16009.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.053774 restraints weight = 11716.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.054273 restraints weight = 9380.397| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15250 Z= 0.184 Angle : 0.666 6.499 20705 Z= 0.315 Chirality : 0.049 0.161 2305 Planarity : 0.004 0.037 2630 Dihedral : 8.970 99.621 2210 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.29 % Allowed : 9.65 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.19), residues: 1830 helix: -1.41 (0.21), residues: 595 sheet: -1.68 (0.27), residues: 355 loop : -1.83 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.010 0.001 TYR E 294 PHE 0.010 0.001 PHE A 200 TRP 0.006 0.001 TRP D 340 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00443 (15245) covalent geometry : angle 0.66601 (20705) hydrogen bonds : bond 0.04336 ( 316) hydrogen bonds : angle 4.99646 ( 858) Misc. bond : bond 0.00010 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.528 Fit side-chains REVERT: A 124 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8379 (m-10) REVERT: A 283 MET cc_start: 0.8856 (tpp) cc_final: 0.8592 (tpp) REVERT: B 244 ASP cc_start: 0.7567 (t0) cc_final: 0.7323 (m-30) REVERT: B 269 MET cc_start: 0.8873 (ttm) cc_final: 0.8650 (ttm) REVERT: B 283 MET cc_start: 0.8874 (tpp) cc_final: 0.8065 (tpp) REVERT: B 304 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8983 (m) REVERT: B 349 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8789 (mp) REVERT: C 124 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8630 (m-10) REVERT: C 349 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8824 (mp) REVERT: E 236 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8684 (pt) REVERT: E 283 MET cc_start: 0.8849 (tpp) cc_final: 0.8625 (tpp) outliers start: 36 outliers final: 26 residues processed: 132 average time/residue: 0.1123 time to fit residues: 23.0916 Evaluate side-chains 128 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.060173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.050357 restraints weight = 46438.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.051925 restraints weight = 24722.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.053009 restraints weight = 15963.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.053746 restraints weight = 11678.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.054233 restraints weight = 9355.583| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15250 Z= 0.170 Angle : 0.657 7.295 20705 Z= 0.310 Chirality : 0.049 0.162 2305 Planarity : 0.004 0.036 2630 Dihedral : 8.845 97.850 2210 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.16 % Allowed : 10.48 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.19), residues: 1830 helix: -1.27 (0.21), residues: 595 sheet: -1.68 (0.27), residues: 355 loop : -1.77 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.009 0.001 TYR E 294 PHE 0.009 0.001 PHE C 200 TRP 0.008 0.001 TRP D 340 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00410 (15245) covalent geometry : angle 0.65684 (20705) hydrogen bonds : bond 0.04172 ( 316) hydrogen bonds : angle 4.93122 ( 858) Misc. bond : bond 0.00009 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.604 Fit side-chains REVERT: A 124 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8355 (m-10) REVERT: A 283 MET cc_start: 0.8828 (tpp) cc_final: 0.8554 (tpp) REVERT: B 269 MET cc_start: 0.8856 (ttm) cc_final: 0.8636 (ttm) REVERT: B 283 MET cc_start: 0.8864 (tpp) cc_final: 0.8082 (tpp) REVERT: B 349 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8841 (mp) REVERT: B 355 MET cc_start: 0.8383 (mmm) cc_final: 0.8097 (mtp) REVERT: C 124 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8637 (m-10) REVERT: C 190 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8367 (ptp) REVERT: C 349 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8901 (mp) REVERT: D 82 MET cc_start: 0.8622 (mmm) cc_final: 0.8260 (tpt) REVERT: E 236 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8657 (pt) REVERT: E 283 MET cc_start: 0.8811 (tpp) cc_final: 0.8600 (tpp) REVERT: E 325 MET cc_start: 0.7769 (mmt) cc_final: 0.7504 (mmt) outliers start: 34 outliers final: 24 residues processed: 124 average time/residue: 0.1089 time to fit residues: 21.3615 Evaluate side-chains 123 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 169 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 76 optimal weight: 0.0370 chunk 25 optimal weight: 9.9990 chunk 72 optimal weight: 0.0000 chunk 109 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 overall best weight: 4.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.060938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.050973 restraints weight = 46382.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.052635 restraints weight = 23899.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.053754 restraints weight = 15130.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.054524 restraints weight = 10971.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.054933 restraints weight = 8700.809| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15250 Z= 0.134 Angle : 0.623 6.552 20705 Z= 0.291 Chirality : 0.047 0.162 2305 Planarity : 0.004 0.034 2630 Dihedral : 8.589 95.866 2210 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.78 % Allowed : 11.05 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.19), residues: 1830 helix: -1.05 (0.22), residues: 595 sheet: -1.63 (0.27), residues: 355 loop : -1.69 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.008 0.001 TYR E 240 PHE 0.008 0.001 PHE E 200 TRP 0.007 0.001 TRP B 340 HIS 0.002 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00321 (15245) covalent geometry : angle 0.62346 (20705) hydrogen bonds : bond 0.03651 ( 316) hydrogen bonds : angle 4.71959 ( 858) Misc. bond : bond 0.00007 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8455 (m-10) REVERT: A 283 MET cc_start: 0.8805 (tpp) cc_final: 0.8546 (tpp) REVERT: B 269 MET cc_start: 0.8920 (ttm) cc_final: 0.8653 (ttm) REVERT: B 283 MET cc_start: 0.8826 (tpp) cc_final: 0.8034 (mpp) REVERT: B 349 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (mp) REVERT: B 355 MET cc_start: 0.8493 (mmm) cc_final: 0.8029 (mtp) REVERT: C 124 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8540 (m-10) REVERT: C 190 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8375 (ptp) REVERT: C 349 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8820 (mp) REVERT: D 82 MET cc_start: 0.8649 (mmm) cc_final: 0.8290 (tpt) REVERT: E 236 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8668 (pt) outliers start: 28 outliers final: 21 residues processed: 118 average time/residue: 0.0993 time to fit residues: 18.5305 Evaluate side-chains 122 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 148 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.058472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.048636 restraints weight = 47511.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.050171 restraints weight = 25384.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.051234 restraints weight = 16459.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.051959 restraints weight = 12059.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.052453 restraints weight = 9686.162| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15250 Z= 0.269 Angle : 0.751 6.846 20705 Z= 0.360 Chirality : 0.053 0.192 2305 Planarity : 0.005 0.041 2630 Dihedral : 9.092 101.525 2210 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.29 % Allowed : 10.67 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.19), residues: 1830 helix: -1.35 (0.20), residues: 595 sheet: -1.82 (0.27), residues: 355 loop : -1.76 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 372 TYR 0.021 0.002 TYR E 279 PHE 0.012 0.002 PHE C 200 TRP 0.008 0.002 TRP E 340 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00646 (15245) covalent geometry : angle 0.75117 (20705) hydrogen bonds : bond 0.05324 ( 316) hydrogen bonds : angle 5.41390 ( 858) Misc. bond : bond 0.00020 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8385 (m-10) REVERT: A 349 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.9008 (mp) REVERT: B 283 MET cc_start: 0.8904 (tpp) cc_final: 0.8050 (mpp) REVERT: B 349 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8804 (mp) REVERT: B 355 MET cc_start: 0.8480 (mmm) cc_final: 0.8097 (mtp) REVERT: C 124 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8673 (m-10) REVERT: C 190 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8458 (ptp) REVERT: C 349 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8837 (mp) REVERT: E 236 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8658 (pt) REVERT: E 283 MET cc_start: 0.8673 (tpp) cc_final: 0.8266 (ttm) outliers start: 36 outliers final: 23 residues processed: 125 average time/residue: 0.1119 time to fit residues: 21.5946 Evaluate side-chains 126 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 120 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 147 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.059514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.049691 restraints weight = 46976.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.051258 restraints weight = 24939.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.052329 restraints weight = 16076.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.053055 restraints weight = 11777.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.053551 restraints weight = 9446.231| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15250 Z= 0.184 Angle : 0.676 6.644 20705 Z= 0.320 Chirality : 0.049 0.162 2305 Planarity : 0.004 0.038 2630 Dihedral : 8.957 99.941 2210 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.03 % Allowed : 11.17 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.19), residues: 1830 helix: -1.18 (0.21), residues: 595 sheet: -1.77 (0.27), residues: 355 loop : -1.74 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 372 TYR 0.014 0.001 TYR E 279 PHE 0.021 0.001 PHE E 375 TRP 0.008 0.001 TRP D 340 HIS 0.003 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00442 (15245) covalent geometry : angle 0.67644 (20705) hydrogen bonds : bond 0.04358 ( 316) hydrogen bonds : angle 5.05043 ( 858) Misc. bond : bond 0.00014 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8446 (m-10) REVERT: A 283 MET cc_start: 0.8862 (tpp) cc_final: 0.8560 (tpp) REVERT: B 283 MET cc_start: 0.8869 (tpp) cc_final: 0.8039 (mpp) REVERT: B 355 MET cc_start: 0.8482 (mmm) cc_final: 0.8034 (mtt) REVERT: C 124 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: C 190 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8404 (ptp) REVERT: C 349 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8917 (mp) REVERT: E 236 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8638 (pt) REVERT: E 283 MET cc_start: 0.8697 (tpp) cc_final: 0.8286 (ttm) outliers start: 32 outliers final: 23 residues processed: 122 average time/residue: 0.1035 time to fit residues: 20.3405 Evaluate side-chains 124 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 96 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.061122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.051319 restraints weight = 46191.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.052911 restraints weight = 24387.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.053996 restraints weight = 15650.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.054737 restraints weight = 11464.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.055234 restraints weight = 9164.775| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15250 Z= 0.118 Angle : 0.616 6.669 20705 Z= 0.286 Chirality : 0.047 0.167 2305 Planarity : 0.004 0.044 2630 Dihedral : 8.508 95.518 2210 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.84 % Allowed : 11.24 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.19), residues: 1830 helix: -0.89 (0.22), residues: 595 sheet: -1.65 (0.27), residues: 355 loop : -1.67 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 210 TYR 0.013 0.001 TYR C 279 PHE 0.009 0.001 PHE D 375 TRP 0.007 0.001 TRP B 340 HIS 0.002 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00279 (15245) covalent geometry : angle 0.61611 (20705) hydrogen bonds : bond 0.03288 ( 316) hydrogen bonds : angle 4.61759 ( 858) Misc. bond : bond 0.00008 ( 5) =============================================================================== Job complete usr+sys time: 1736.54 seconds wall clock time: 30 minutes 53.26 seconds (1853.26 seconds total)