Starting phenix.real_space_refine on Sat Aug 8 05:33:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12bx_76299/08_2026/12bx_76299.cif Found real_map, /net/cci-nas-00/data/ceres_data/12bx_76299/08_2026/12bx_76299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12bx_76299/08_2026/12bx_76299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12bx_76299/08_2026/12bx_76299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12bx_76299/08_2026/12bx_76299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12bx_76299/08_2026/12bx_76299.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 16 5.49 5 Mg 8 5.21 5 S 174 5.16 5 C 15906 2.51 5 N 4278 2.21 5 O 4852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25236 Number of models: 1 Model: "" Number of chains: 18 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: "B" 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: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: "D" 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: "E" 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: 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: "G" 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: "H" 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: "I" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1793 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 217} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.36, per 1000 atoms: 0.21 Number of scatterers: 25236 At special positions: 0 Unit cell: (88.56, 120.96, 279.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 174 16.00 P 16 15.00 Mg 8 11.99 O 4852 8.00 N 4278 7.00 C 15906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5914 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 50 sheets defined 50.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.718A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.791A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.733A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.532A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 355 removed outlier: 6.372A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.674A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.785A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.878A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.742A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 349 No H-bonds generated for 'chain 'B' and resid 348 through 349' Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.930A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.917A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.558A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.786A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.664A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.637A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.618A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.764A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.553A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.546A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 349 No H-bonds generated for 'chain 'D' and resid 348 through 349' Processing helix chain 'D' and resid 350 through 355 removed outlier: 4.048A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.719A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.631A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.852A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.526A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.593A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 348 through 349 No H-bonds generated for 'chain 'E' and resid 348 through 349' Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.937A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.627A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.868A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.593A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'F' and resid 348 through 349 No H-bonds generated for 'chain 'F' and resid 348 through 349' Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.830A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 removed outlier: 3.608A pdb=" N CYS F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 93 Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.838A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.153A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 348 removed outlier: 3.636A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 355 removed outlier: 3.982A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 removed outlier: 3.772A pdb=" N CYS G 374 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 93 removed outlier: 3.551A pdb=" N GLU H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.961A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.941A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 260 Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 261 through 262 No H-bonds generated for 'chain 'H' and resid 261 through 262' Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 295 removed outlier: 3.652A pdb=" N ARG H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.250A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 347 Processing helix chain 'H' and resid 348 through 349 No H-bonds generated for 'chain 'H' and resid 348 through 349' Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.899A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 removed outlier: 3.569A pdb=" N CYS H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 225 removed outlier: 3.504A pdb=" N ARG I 225 " --> pdb=" O ARG I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 248 Processing helix chain 'I' and resid 261 through 269 removed outlier: 3.888A pdb=" N ALA I 265 " --> pdb=" O ALA I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 342 removed outlier: 3.932A pdb=" N ILE I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR I 340 " --> pdb=" O SER I 336 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET I 342 " --> pdb=" O PHE I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.620A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.049A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (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 29 through 32 removed outlier: 6.403A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.551A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.028A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.058A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.728A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.085A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.159A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 103 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.592A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.918A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.855A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.461A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 176 through 178 removed outlier: 4.113A pdb=" N GLN G 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.917A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 176 through 178 removed outlier: 6.218A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 176 through 178 removed outlier: 3.911A pdb=" N GLN H 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.402A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET G 132 " --> pdb=" O ILE G 357 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 7.183A pdb=" N VAL G 298 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.820A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.490A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AF4, first strand: chain 'I' and resid 172 through 175 Processing sheet with id=AF5, first strand: chain 'I' and resid 285 through 289 removed outlier: 6.350A pdb=" N LEU I 287 " --> pdb=" O LYS I 275 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS I 275 " --> pdb=" O LEU I 287 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE I 315 " --> pdb=" O SER I 351 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU I 353 " --> pdb=" O ILE I 315 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL I 317 " --> pdb=" O LEU I 353 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7880 1.33 - 1.45: 3855 1.45 - 1.57: 13717 1.57 - 1.69: 25 1.69 - 1.81: 305 Bond restraints: 25782 Sorted by residual: bond pdb=" CA ASP I 259 " pdb=" C ASP I 259 " ideal model delta sigma weight residual 1.526 1.560 -0.034 1.30e-02 5.92e+03 6.86e+00 bond pdb=" CA THR I 257 " pdb=" C THR I 257 " ideal model delta sigma weight residual 1.522 1.552 -0.029 1.20e-02 6.94e+03 5.89e+00 bond pdb=" C ASN G 12 " pdb=" N GLY G 13 " ideal model delta sigma weight residual 1.332 1.300 0.031 1.54e-02 4.22e+03 4.14e+00 bond pdb=" C ASN E 12 " pdb=" N GLY E 13 " ideal model delta sigma weight residual 1.328 1.302 0.026 1.34e-02 5.57e+03 3.85e+00 bond pdb=" CG LEU I 273 " pdb=" CD1 LEU I 273 " ideal model delta sigma weight residual 1.521 1.586 -0.065 3.30e-02 9.18e+02 3.85e+00 ... (remaining 25777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 33208 1.47 - 2.93: 1381 2.93 - 4.40: 270 4.40 - 5.86: 101 5.86 - 7.33: 19 Bond angle restraints: 34979 Sorted by residual: angle pdb=" C GLY I 297 " pdb=" N ALA I 298 " pdb=" CA ALA I 298 " ideal model delta sigma weight residual 120.38 125.28 -4.90 1.37e+00 5.33e-01 1.28e+01 angle pdb=" CA GLY I 167 " pdb=" C GLY I 167 " pdb=" N ARG I 168 " ideal model delta sigma weight residual 114.23 117.35 -3.12 8.80e-01 1.29e+00 1.26e+01 angle pdb=" N ASP I 259 " pdb=" CA ASP I 259 " pdb=" C ASP I 259 " ideal model delta sigma weight residual 107.62 114.21 -6.59 1.97e+00 2.58e-01 1.12e+01 angle pdb=" CA THR I 257 " pdb=" CB THR I 257 " pdb=" CG2 THR I 257 " ideal model delta sigma weight residual 110.50 116.12 -5.62 1.70e+00 3.46e-01 1.09e+01 angle pdb=" N GLU I 258 " pdb=" CA GLU I 258 " pdb=" CB GLU I 258 " ideal model delta sigma weight residual 110.46 105.35 5.11 1.55e+00 4.16e-01 1.09e+01 ... (remaining 34974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 14725 22.25 - 44.49: 632 44.49 - 66.74: 119 66.74 - 88.98: 31 88.98 - 111.23: 7 Dihedral angle restraints: 15514 sinusoidal: 6279 harmonic: 9235 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 51.23 -111.23 1 2.00e+01 2.50e-03 3.27e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 46.49 -106.49 1 2.00e+01 2.50e-03 3.08e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 45.23 -105.22 1 2.00e+01 2.50e-03 3.03e+01 ... (remaining 15511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2032 0.035 - 0.070: 1188 0.070 - 0.104: 462 0.104 - 0.139: 181 0.139 - 0.174: 11 Chirality restraints: 3874 Sorted by residual: chirality pdb=" CA VAL I 276 " pdb=" N VAL I 276 " pdb=" C VAL I 276 " pdb=" CB VAL I 276 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA THR I 260 " pdb=" N THR I 260 " pdb=" C THR I 260 " pdb=" CB THR I 260 " both_signs ideal model delta sigma weight residual False 2.53 2.69 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" C2' ADP D 401 " pdb=" C1' ADP D 401 " pdb=" C3' ADP D 401 " pdb=" O2' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 3871 not shown) Planarity restraints: 4484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.64e+00 pdb=" N PRO B 164 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 153 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO I 154 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO I 154 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 154 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 259 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C ASP I 259 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP I 259 " -0.013 2.00e-02 2.50e+03 pdb=" N THR I 260 " -0.012 2.00e-02 2.50e+03 ... (remaining 4481 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 20 2.53 - 3.12: 18840 3.12 - 3.71: 37947 3.71 - 4.31: 54704 4.31 - 4.90: 93215 Nonbonded interactions: 204726 Sorted by model distance: nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.935 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.959 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 1.964 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.973 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.980 2.170 ... (remaining 204721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 5 through 402) selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.860 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.007 0.065 25782 Z= 0.323 Angle : 0.756 7.331 34979 Z= 0.401 Chirality : 0.051 0.174 3874 Planarity : 0.006 0.059 4484 Dihedral : 13.486 111.228 9600 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.00 % Allowed : 7.34 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3157 helix: 0.17 (0.15), residues: 1240 sheet: -0.07 (0.20), residues: 627 loop : 0.47 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 268 TYR 0.016 0.002 TYR F 133 PHE 0.027 0.002 PHE I 365 TRP 0.022 0.002 TRP E 79 HIS 0.007 0.002 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.32 (25782) covalent geometry : angle 0.75621 / 0.40 (34979) hydrogen bonds : bond 0.17568 / 12.07 ( 1262) hydrogen bonds : angle 6.87502 / 4.82 ( 3237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7314 (mmmt) REVERT: A 82 MET cc_start: 0.9507 (tpt) cc_final: 0.9266 (tpp) REVERT: A 86 TRP cc_start: 0.9368 (m-10) cc_final: 0.8586 (m-90) REVERT: A 176 MET cc_start: 0.8964 (mmt) cc_final: 0.8620 (mmp) REVERT: A 217 CYS cc_start: 0.8121 (m) cc_final: 0.7688 (m) REVERT: A 355 MET cc_start: 0.8740 (mtt) cc_final: 0.8459 (ttt) REVERT: B 44 MET cc_start: 0.8843 (mtp) cc_final: 0.8504 (pmm) REVERT: B 82 MET cc_start: 0.8951 (tpt) cc_final: 0.8718 (tpp) REVERT: B 222 ASP cc_start: 0.8390 (t0) cc_final: 0.7715 (p0) REVERT: C 132 MET cc_start: 0.9161 (ppp) cc_final: 0.8917 (ppp) REVERT: C 314 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: C 372 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8163 (ptp-170) REVERT: D 211 ASP cc_start: 0.8613 (t70) cc_final: 0.8389 (m-30) REVERT: D 227 MET cc_start: 0.8806 (mmm) cc_final: 0.8395 (mmm) REVERT: D 314 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8928 (tp40) REVERT: D 361 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8104 (mt-10) REVERT: E 50 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8669 (tppt) REVERT: E 83 GLU cc_start: 0.9168 (tt0) cc_final: 0.8906 (tm-30) REVERT: E 93 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8030 (mp0) REVERT: E 123 MET cc_start: 0.8717 (mmt) cc_final: 0.8494 (mmm) REVERT: E 227 MET cc_start: 0.8496 (mmm) cc_final: 0.8060 (mmm) REVERT: E 229 THR cc_start: 0.8723 (m) cc_final: 0.8384 (p) REVERT: E 314 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: E 360 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8936 (pp30) REVERT: F 118 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8207 (ttpt) REVERT: F 167 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8301 (tm-30) REVERT: F 227 MET cc_start: 0.8756 (mmm) cc_final: 0.8397 (mmm) REVERT: F 325 MET cc_start: 0.8982 (mmp) cc_final: 0.8651 (mmp) REVERT: G 82 MET cc_start: 0.8355 (tpt) cc_final: 0.7980 (tpt) REVERT: G 123 MET cc_start: 0.9186 (mmt) cc_final: 0.8984 (mmm) REVERT: G 132 MET cc_start: 0.9242 (ppp) cc_final: 0.9021 (ppp) REVERT: G 176 MET cc_start: 0.8410 (mmt) cc_final: 0.8189 (mmm) REVERT: G 297 ASN cc_start: 0.8937 (m110) cc_final: 0.8689 (m-40) REVERT: G 305 MET cc_start: 0.9174 (mmm) cc_final: 0.8616 (tpp) REVERT: G 369 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8554 (tp) REVERT: H 176 MET cc_start: 0.7825 (mmt) cc_final: 0.7367 (mmm) REVERT: H 276 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9015 (tp30) REVERT: H 305 MET cc_start: 0.8879 (mmm) cc_final: 0.8517 (mmt) REVERT: H 355 MET cc_start: 0.9466 (mtt) cc_final: 0.9143 (mpp) REVERT: I 160 GLN cc_start: 0.8566 (tt0) cc_final: 0.8049 (mp10) REVERT: I 164 GLN cc_start: 0.8296 (tt0) cc_final: 0.7750 (tm-30) REVERT: I 165 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8385 (m) REVERT: I 189 PHE cc_start: 0.8242 (m-80) cc_final: 0.7731 (m-80) REVERT: I 215 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8798 (tm-30) REVERT: I 243 MET cc_start: 0.9198 (mtp) cc_final: 0.8993 (mtm) REVERT: I 245 GLN cc_start: 0.9544 (tm-30) cc_final: 0.9315 (tm-30) REVERT: I 274 TYR cc_start: 0.8325 (m-80) cc_final: 0.7797 (m-80) REVERT: I 309 HIS cc_start: 0.8989 (t70) cc_final: 0.8103 (t70) REVERT: I 342 MET cc_start: 0.8563 (mpp) cc_final: 0.8114 (mpp) REVERT: I 369 TRP cc_start: 0.6996 (t-100) cc_final: 0.5889 (t-100) outliers start: 81 outliers final: 15 residues processed: 371 average time/residue: 0.1656 time to fit residues: 96.2743 Evaluate side-chains 224 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 215 GLN Chi-restraints excluded: chain I residue 272 LYS Chi-restraints excluded: chain I residue 352 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 92 ASN A 275 HIS A 360 GLN B 92 ASN B 246 GLN B 275 HIS C 92 ASN C 161 HIS C 275 HIS D 92 ASN D 246 GLN E 12 ASN E 92 ASN E 246 GLN E 275 HIS E 360 GLN F 92 ASN F 128 ASN F 161 HIS F 246 GLN F 275 HIS G 92 ASN G 128 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN ** H 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS I 155 ASN ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 GLN I 347 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059575 restraints weight = 76924.565| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.24 r_work: 0.2958 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25782 Z= 0.134 Angle : 0.596 12.884 34979 Z= 0.297 Chirality : 0.044 0.150 3874 Planarity : 0.004 0.047 4484 Dihedral : 7.149 95.392 3642 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.48 % Allowed : 10.67 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 3157 helix: 0.84 (0.15), residues: 1249 sheet: 0.23 (0.20), residues: 618 loop : 0.70 (0.19), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 372 TYR 0.010 0.001 TYR G 166 PHE 0.031 0.001 PHE I 365 TRP 0.013 0.001 TRP E 79 HIS 0.006 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (25782) covalent geometry : angle 0.59605 / 0.30 (34979) hydrogen bonds : bond 0.03926 / 2.68 ( 1262) hydrogen bonds : angle 5.06592 / 3.56 ( 3237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7597 (mmmt) REVERT: A 80 ASP cc_start: 0.9343 (m-30) cc_final: 0.9129 (p0) REVERT: A 82 MET cc_start: 0.9486 (tpt) cc_final: 0.9268 (tpp) REVERT: A 86 TRP cc_start: 0.9165 (m-10) cc_final: 0.8589 (m-90) REVERT: A 107 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7341 (pt0) REVERT: A 123 MET cc_start: 0.9184 (tpp) cc_final: 0.8798 (tpp) REVERT: A 217 CYS cc_start: 0.7479 (m) cc_final: 0.7120 (m) REVERT: B 82 MET cc_start: 0.8985 (tpt) cc_final: 0.8761 (tpp) REVERT: B 222 ASP cc_start: 0.8269 (t0) cc_final: 0.7573 (p0) REVERT: C 3 ASP cc_start: 0.1816 (OUTLIER) cc_final: 0.1570 (p0) REVERT: C 132 MET cc_start: 0.8690 (ppp) cc_final: 0.8478 (ppp) REVERT: D 211 ASP cc_start: 0.8634 (t70) cc_final: 0.8432 (m-30) REVERT: D 226 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8007 (tt0) REVERT: D 325 MET cc_start: 0.9067 (mmp) cc_final: 0.8613 (mmp) REVERT: D 361 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8052 (mt-10) REVERT: E 50 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8775 (tppt) REVERT: E 93 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8123 (mp0) REVERT: E 229 THR cc_start: 0.8780 (m) cc_final: 0.8458 (p) REVERT: E 314 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: F 118 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8258 (tttt) REVERT: F 167 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8101 (tm-30) REVERT: F 227 MET cc_start: 0.8816 (mmm) cc_final: 0.8440 (mmm) REVERT: F 325 MET cc_start: 0.9073 (mmp) cc_final: 0.8681 (mmp) REVERT: G 44 MET cc_start: 0.8862 (mtp) cc_final: 0.8635 (mtt) REVERT: G 82 MET cc_start: 0.8395 (tpt) cc_final: 0.8174 (tpt) REVERT: G 176 MET cc_start: 0.8356 (mmt) cc_final: 0.7980 (mmm) REVERT: G 297 ASN cc_start: 0.8807 (m110) cc_final: 0.8597 (m110) REVERT: G 338 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8845 (m) REVERT: H 176 MET cc_start: 0.7863 (mmt) cc_final: 0.7214 (mmm) REVERT: H 227 MET cc_start: 0.9153 (mmt) cc_final: 0.8735 (tpp) REVERT: H 276 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9092 (tp30) REVERT: H 355 MET cc_start: 0.9422 (mtt) cc_final: 0.9118 (mpp) REVERT: I 160 GLN cc_start: 0.8495 (tt0) cc_final: 0.7963 (mm-40) REVERT: I 174 THR cc_start: 0.8442 (m) cc_final: 0.8148 (p) REVERT: I 270 LEU cc_start: 0.8618 (mt) cc_final: 0.8097 (mt) REVERT: I 274 TYR cc_start: 0.8353 (m-80) cc_final: 0.7893 (m-80) REVERT: I 283 MET cc_start: 0.7055 (tpp) cc_final: 0.6826 (tpp) REVERT: I 309 HIS cc_start: 0.8883 (t70) cc_final: 0.7988 (t70) REVERT: I 369 TRP cc_start: 0.7032 (t-100) cc_final: 0.5679 (t-100) outliers start: 40 outliers final: 19 residues processed: 233 average time/residue: 0.1476 time to fit residues: 56.9891 Evaluate side-chains 216 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 272 LYS Chi-restraints excluded: chain I residue 294 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 164 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 91 optimal weight: 0.0980 chunk 268 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 128 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 HIS ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.075745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.056084 restraints weight = 77337.531| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.19 r_work: 0.2892 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25782 Z= 0.204 Angle : 0.611 7.647 34979 Z= 0.306 Chirality : 0.045 0.149 3874 Planarity : 0.004 0.049 4484 Dihedral : 6.666 96.159 3606 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.70 % Allowed : 11.63 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 3157 helix: 0.75 (0.15), residues: 1332 sheet: 0.23 (0.20), residues: 618 loop : 0.53 (0.19), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 225 TYR 0.010 0.001 TYR F 240 PHE 0.014 0.001 PHE I 365 TRP 0.014 0.002 TRP E 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (25782) covalent geometry : angle 0.61133 / 0.31 (34979) hydrogen bonds : bond 0.04233 / 2.88 ( 1262) hydrogen bonds : angle 4.90867 / 3.46 ( 3237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.1629 (pmm) cc_final: 0.1359 (pmm) REVERT: A 50 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7641 (mmmt) REVERT: A 80 ASP cc_start: 0.9348 (m-30) cc_final: 0.9107 (p0) REVERT: A 107 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: A 123 MET cc_start: 0.9266 (tpp) cc_final: 0.8895 (tpp) REVERT: A 217 CYS cc_start: 0.7496 (m) cc_final: 0.7189 (m) REVERT: A 355 MET cc_start: 0.8875 (ttt) cc_final: 0.8469 (ttt) REVERT: B 40 HIS cc_start: 0.4393 (t-90) cc_final: 0.4184 (t-90) REVERT: B 222 ASP cc_start: 0.8368 (t0) cc_final: 0.7747 (p0) REVERT: C 132 MET cc_start: 0.8876 (ppp) cc_final: 0.8393 (ppp) REVERT: D 211 ASP cc_start: 0.8674 (t70) cc_final: 0.8471 (m-30) REVERT: D 226 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8206 (tt0) REVERT: D 361 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7969 (mt-10) REVERT: E 50 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8777 (tppt) REVERT: E 227 MET cc_start: 0.8554 (mmm) cc_final: 0.8176 (mmm) REVERT: E 314 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (tt0) REVERT: E 345 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9053 (mp) REVERT: F 167 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8156 (tm-30) REVERT: F 176 MET cc_start: 0.8735 (mmt) cc_final: 0.8513 (mmm) REVERT: F 227 MET cc_start: 0.8803 (mmm) cc_final: 0.8452 (mmm) REVERT: F 305 MET cc_start: 0.9283 (mmm) cc_final: 0.8991 (tpp) REVERT: F 314 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7833 (tp40) REVERT: G 82 MET cc_start: 0.8474 (tpt) cc_final: 0.8214 (tpt) REVERT: G 176 MET cc_start: 0.8458 (mmt) cc_final: 0.7958 (mmm) REVERT: G 338 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.8882 (m) REVERT: H 176 MET cc_start: 0.7941 (mmt) cc_final: 0.7274 (mmm) REVERT: H 227 MET cc_start: 0.9131 (mmt) cc_final: 0.8687 (tpp) REVERT: H 276 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9032 (tp30) REVERT: H 355 MET cc_start: 0.9422 (mtt) cc_final: 0.9119 (mpp) REVERT: I 270 LEU cc_start: 0.8885 (mt) cc_final: 0.8597 (mt) REVERT: I 273 LEU cc_start: 0.8770 (tt) cc_final: 0.7912 (mt) REVERT: I 274 TYR cc_start: 0.8183 (m-80) cc_final: 0.7675 (m-80) REVERT: I 369 TRP cc_start: 0.7137 (t-100) cc_final: 0.5933 (t-100) outliers start: 46 outliers final: 23 residues processed: 229 average time/residue: 0.1418 time to fit residues: 54.6793 Evaluate side-chains 215 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 217 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 195 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.056460 restraints weight = 77347.302| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.20 r_work: 0.2895 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25782 Z= 0.166 Angle : 0.574 6.786 34979 Z= 0.284 Chirality : 0.044 0.138 3874 Planarity : 0.004 0.052 4484 Dihedral : 6.392 90.378 3602 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.78 % Allowed : 12.45 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3157 helix: 0.91 (0.15), residues: 1332 sheet: 0.25 (0.20), residues: 618 loop : 0.54 (0.19), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 372 TYR 0.008 0.001 TYR F 240 PHE 0.019 0.001 PHE H 124 TRP 0.014 0.002 TRP I 318 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (25782) covalent geometry : angle 0.57413 / 0.28 (34979) hydrogen bonds : bond 0.03682 / 2.51 ( 1262) hydrogen bonds : angle 4.74116 / 3.33 ( 3237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2110 (pmm) cc_final: 0.1697 (pmm) REVERT: A 107 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: A 123 MET cc_start: 0.9369 (tpp) cc_final: 0.9060 (tpp) REVERT: A 217 CYS cc_start: 0.7531 (m) cc_final: 0.7164 (m) REVERT: A 355 MET cc_start: 0.8871 (ttt) cc_final: 0.8325 (ttt) REVERT: B 82 MET cc_start: 0.8976 (tpt) cc_final: 0.8603 (tpp) REVERT: B 222 ASP cc_start: 0.8335 (t0) cc_final: 0.7850 (p0) REVERT: D 123 MET cc_start: 0.8418 (tpp) cc_final: 0.8206 (tpp) REVERT: D 211 ASP cc_start: 0.8674 (t70) cc_final: 0.8464 (m-30) REVERT: D 226 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8227 (tt0) REVERT: D 361 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8061 (mt-10) REVERT: E 45 VAL cc_start: 0.9049 (m) cc_final: 0.8798 (p) REVERT: E 50 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8771 (tppt) REVERT: E 345 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9085 (mp) REVERT: F 167 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8150 (tm-30) REVERT: F 176 MET cc_start: 0.8726 (mmt) cc_final: 0.8492 (mmm) REVERT: F 227 MET cc_start: 0.8799 (mmm) cc_final: 0.8437 (mmm) REVERT: F 314 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7815 (tp40) REVERT: G 82 MET cc_start: 0.8477 (tpt) cc_final: 0.8243 (tpt) REVERT: G 83 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8561 (pp20) REVERT: G 176 MET cc_start: 0.8458 (mmt) cc_final: 0.7960 (mmm) REVERT: G 338 SER cc_start: 0.9254 (OUTLIER) cc_final: 0.8867 (m) REVERT: H 176 MET cc_start: 0.7892 (mmt) cc_final: 0.7207 (mmm) REVERT: H 276 GLU cc_start: 0.9559 (mt-10) cc_final: 0.9020 (tp30) REVERT: H 305 MET cc_start: 0.8996 (tpp) cc_final: 0.8386 (mmt) REVERT: H 355 MET cc_start: 0.9433 (mtt) cc_final: 0.9151 (mpp) REVERT: I 174 THR cc_start: 0.8370 (m) cc_final: 0.8041 (p) REVERT: I 243 MET cc_start: 0.9107 (ptp) cc_final: 0.8833 (ptp) REVERT: I 270 LEU cc_start: 0.8942 (mt) cc_final: 0.8695 (mt) REVERT: I 274 TYR cc_start: 0.8139 (m-80) cc_final: 0.7767 (m-80) REVERT: I 283 MET cc_start: 0.7184 (tpp) cc_final: 0.6882 (tpp) REVERT: I 328 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7553 (mtm-85) REVERT: I 369 TRP cc_start: 0.7167 (t-100) cc_final: 0.6010 (t-100) outliers start: 48 outliers final: 30 residues processed: 236 average time/residue: 0.1440 time to fit residues: 57.3815 Evaluate side-chains 225 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 104 optimal weight: 0.9990 chunk 268 optimal weight: 0.4980 chunk 3 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 271 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 275 HIS ** I 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.076704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057191 restraints weight = 76538.974| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.19 r_work: 0.2913 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25782 Z= 0.123 Angle : 0.551 8.326 34979 Z= 0.268 Chirality : 0.043 0.138 3874 Planarity : 0.004 0.045 4484 Dihedral : 6.057 83.306 3594 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.82 % Allowed : 12.86 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 3157 helix: 1.09 (0.15), residues: 1325 sheet: 0.30 (0.20), residues: 618 loop : 0.63 (0.19), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 372 TYR 0.008 0.001 TYR A 133 PHE 0.014 0.001 PHE I 362 TRP 0.016 0.001 TRP I 318 HIS 0.005 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (25782) covalent geometry : angle 0.55058 / 0.27 (34979) hydrogen bonds : bond 0.03305 / 2.26 ( 1262) hydrogen bonds : angle 4.59947 / 3.23 ( 3237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2290 (pmm) cc_final: 0.1860 (pmm) REVERT: A 82 MET cc_start: 0.9637 (tpp) cc_final: 0.8909 (tpp) REVERT: A 86 TRP cc_start: 0.9025 (m-10) cc_final: 0.8790 (m-90) REVERT: A 107 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: A 123 MET cc_start: 0.9382 (tpp) cc_final: 0.9006 (tpp) REVERT: A 217 CYS cc_start: 0.7503 (m) cc_final: 0.7080 (m) REVERT: A 305 MET cc_start: 0.8983 (tpp) cc_final: 0.8767 (mmt) REVERT: A 313 MET cc_start: 0.9548 (tpp) cc_final: 0.9338 (mmt) REVERT: A 355 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8344 (ttt) REVERT: B 82 MET cc_start: 0.8991 (tpt) cc_final: 0.8561 (tpp) REVERT: B 222 ASP cc_start: 0.8384 (t0) cc_final: 0.7886 (p0) REVERT: C 3 ASP cc_start: 0.2063 (OUTLIER) cc_final: 0.1720 (p0) REVERT: D 226 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8213 (tt0) REVERT: D 361 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8009 (mt-10) REVERT: E 45 VAL cc_start: 0.9058 (m) cc_final: 0.8815 (p) REVERT: E 50 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8759 (tppt) REVERT: E 227 MET cc_start: 0.8530 (mmm) cc_final: 0.8173 (mmm) REVERT: E 345 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9059 (mp) REVERT: F 167 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8220 (tm-30) REVERT: F 176 MET cc_start: 0.8720 (mmt) cc_final: 0.8481 (mmm) REVERT: F 227 MET cc_start: 0.8802 (mmm) cc_final: 0.8448 (mmm) REVERT: G 82 MET cc_start: 0.8476 (tpt) cc_final: 0.8264 (tpt) REVERT: G 176 MET cc_start: 0.8410 (mmt) cc_final: 0.8196 (mmm) REVERT: G 338 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8862 (m) REVERT: H 176 MET cc_start: 0.7867 (mmt) cc_final: 0.7233 (mmm) REVERT: H 276 GLU cc_start: 0.9562 (mt-10) cc_final: 0.8945 (tp30) REVERT: H 283 MET cc_start: 0.9231 (mmm) cc_final: 0.9019 (mmm) REVERT: H 305 MET cc_start: 0.8984 (tpp) cc_final: 0.8368 (mmt) REVERT: H 355 MET cc_start: 0.9433 (mtt) cc_final: 0.9145 (mpp) REVERT: I 174 THR cc_start: 0.8437 (m) cc_final: 0.8114 (p) REVERT: I 226 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8466 (p) REVERT: I 243 MET cc_start: 0.9169 (ptp) cc_final: 0.8677 (ptp) REVERT: I 270 LEU cc_start: 0.8861 (mt) cc_final: 0.8618 (mt) REVERT: I 274 TYR cc_start: 0.8199 (m-80) cc_final: 0.7817 (m-80) REVERT: I 283 MET cc_start: 0.7064 (tpp) cc_final: 0.6813 (tpp) REVERT: I 369 TRP cc_start: 0.7158 (t-100) cc_final: 0.6022 (t-100) outliers start: 49 outliers final: 30 residues processed: 232 average time/residue: 0.1417 time to fit residues: 55.8835 Evaluate side-chains 223 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 156 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 299 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 272 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 GLN ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.077473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057006 restraints weight = 77624.078| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.26 r_work: 0.2941 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25782 Z= 0.154 Angle : 0.566 8.757 34979 Z= 0.276 Chirality : 0.043 0.134 3874 Planarity : 0.004 0.043 4484 Dihedral : 5.999 82.457 3594 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.00 % Allowed : 13.12 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 3157 helix: 1.14 (0.15), residues: 1325 sheet: 0.27 (0.20), residues: 618 loop : 0.60 (0.19), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 372 TYR 0.008 0.001 TYR F 240 PHE 0.011 0.001 PHE I 362 TRP 0.019 0.001 TRP I 318 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25782) covalent geometry : angle 0.56584 / 0.28 (34979) hydrogen bonds : bond 0.03510 / 2.39 ( 1262) hydrogen bonds : angle 4.58500 / 3.22 ( 3237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2271 (pmm) cc_final: 0.1831 (pmm) REVERT: A 82 MET cc_start: 0.9616 (tpp) cc_final: 0.8904 (tpp) REVERT: A 86 TRP cc_start: 0.9094 (m-10) cc_final: 0.8840 (m-90) REVERT: A 107 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: A 123 MET cc_start: 0.9392 (tpp) cc_final: 0.9059 (tpp) REVERT: A 217 CYS cc_start: 0.7715 (m) cc_final: 0.7252 (m) REVERT: A 299 MET cc_start: 0.8850 (mtm) cc_final: 0.8584 (mtm) REVERT: A 313 MET cc_start: 0.9547 (tpp) cc_final: 0.9236 (tpt) REVERT: A 355 MET cc_start: 0.8916 (ttt) cc_final: 0.8433 (ttt) REVERT: B 222 ASP cc_start: 0.8383 (t0) cc_final: 0.7994 (p0) REVERT: C 3 ASP cc_start: 0.2376 (OUTLIER) cc_final: 0.2031 (p0) REVERT: D 123 MET cc_start: 0.8301 (tpp) cc_final: 0.8080 (tpp) REVERT: D 226 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8329 (tt0) REVERT: D 325 MET cc_start: 0.9028 (mmp) cc_final: 0.8791 (mmp) REVERT: D 361 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8005 (mt-10) REVERT: E 50 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8825 (tppt) REVERT: E 345 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9162 (mp) REVERT: F 167 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8174 (tm-30) REVERT: F 227 MET cc_start: 0.8895 (mmm) cc_final: 0.8564 (mmm) REVERT: F 314 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7892 (tp40) REVERT: G 82 MET cc_start: 0.8657 (tpt) cc_final: 0.8418 (tpt) REVERT: G 83 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8632 (pp20) REVERT: G 338 SER cc_start: 0.9339 (OUTLIER) cc_final: 0.8958 (m) REVERT: H 123 MET cc_start: 0.9297 (mmm) cc_final: 0.8904 (tpt) REVERT: H 176 MET cc_start: 0.8171 (mmt) cc_final: 0.7512 (mmm) REVERT: H 276 GLU cc_start: 0.9551 (mt-10) cc_final: 0.8960 (tp30) REVERT: H 305 MET cc_start: 0.9031 (tpp) cc_final: 0.8487 (mmt) REVERT: H 355 MET cc_start: 0.9463 (mtt) cc_final: 0.9241 (mpp) REVERT: I 174 THR cc_start: 0.8373 (m) cc_final: 0.8057 (p) REVERT: I 226 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8556 (p) REVERT: I 270 LEU cc_start: 0.8863 (mt) cc_final: 0.8319 (mt) REVERT: I 274 TYR cc_start: 0.8191 (m-80) cc_final: 0.7802 (m-80) REVERT: I 283 MET cc_start: 0.7011 (tpp) cc_final: 0.6810 (tpp) REVERT: I 309 HIS cc_start: 0.8938 (t70) cc_final: 0.8038 (t70) REVERT: I 369 TRP cc_start: 0.7263 (t-100) cc_final: 0.6006 (t-100) outliers start: 54 outliers final: 37 residues processed: 233 average time/residue: 0.1459 time to fit residues: 57.8282 Evaluate side-chains 230 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 346 LYS Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 171 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 317 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 12 ASN ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.075254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056508 restraints weight = 76532.234| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.14 r_work: 0.2947 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25782 Z= 0.153 Angle : 0.565 10.363 34979 Z= 0.275 Chirality : 0.043 0.137 3874 Planarity : 0.004 0.043 4484 Dihedral : 5.912 80.459 3594 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.15 % Allowed : 13.00 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 3157 helix: 1.17 (0.15), residues: 1322 sheet: 0.31 (0.20), residues: 618 loop : 0.56 (0.19), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 372 TYR 0.007 0.001 TYR F 240 PHE 0.010 0.001 PHE H 255 TRP 0.020 0.001 TRP I 318 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (25782) covalent geometry : angle 0.56478 / 0.27 (34979) hydrogen bonds : bond 0.03453 / 2.35 ( 1262) hydrogen bonds : angle 4.55525 / 3.20 ( 3237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2452 (pmm) cc_final: 0.1944 (pmm) REVERT: A 82 MET cc_start: 0.9611 (tpp) cc_final: 0.8899 (tpp) REVERT: A 86 TRP cc_start: 0.9119 (m-10) cc_final: 0.8871 (m-90) REVERT: A 107 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: A 123 MET cc_start: 0.9395 (tpp) cc_final: 0.9078 (tpp) REVERT: A 217 CYS cc_start: 0.7706 (m) cc_final: 0.7190 (m) REVERT: A 313 MET cc_start: 0.9528 (tpp) cc_final: 0.9190 (tpt) REVERT: A 355 MET cc_start: 0.8964 (ttt) cc_final: 0.8564 (ttt) REVERT: B 222 ASP cc_start: 0.8352 (t0) cc_final: 0.7993 (p0) REVERT: C 3 ASP cc_start: 0.2369 (OUTLIER) cc_final: 0.2131 (p0) REVERT: D 123 MET cc_start: 0.8302 (tpp) cc_final: 0.8051 (tpp) REVERT: D 325 MET cc_start: 0.9049 (mmp) cc_final: 0.8775 (mmp) REVERT: D 361 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8040 (mt-10) REVERT: E 50 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8821 (tppt) REVERT: E 227 MET cc_start: 0.8633 (mmm) cc_final: 0.8329 (mmm) REVERT: E 345 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9157 (mp) REVERT: F 167 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8150 (tm-30) REVERT: F 227 MET cc_start: 0.8906 (mmm) cc_final: 0.8574 (mmm) REVERT: F 314 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7904 (tp40) REVERT: G 82 MET cc_start: 0.8671 (tpt) cc_final: 0.8413 (tpt) REVERT: G 83 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8635 (pp20) REVERT: G 338 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.8950 (m) REVERT: H 176 MET cc_start: 0.8141 (mmt) cc_final: 0.7503 (mmm) REVERT: H 276 GLU cc_start: 0.9558 (mt-10) cc_final: 0.8967 (tp30) REVERT: H 305 MET cc_start: 0.9032 (tpp) cc_final: 0.8499 (mmt) REVERT: H 355 MET cc_start: 0.9454 (mtt) cc_final: 0.9231 (mpp) REVERT: I 270 LEU cc_start: 0.8870 (mt) cc_final: 0.8355 (mt) REVERT: I 273 LEU cc_start: 0.8281 (tt) cc_final: 0.7353 (mt) REVERT: I 274 TYR cc_start: 0.8103 (m-80) cc_final: 0.7693 (m-80) REVERT: I 309 HIS cc_start: 0.8890 (t70) cc_final: 0.8062 (t70) REVERT: I 369 TRP cc_start: 0.7294 (t-100) cc_final: 0.5977 (t-100) outliers start: 58 outliers final: 38 residues processed: 233 average time/residue: 0.1484 time to fit residues: 58.8757 Evaluate side-chains 231 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 209 GLU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 346 LYS Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 277 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 232 HIS ** 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 = 0.3488 r_free = 0.3488 target = 0.076568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056060 restraints weight = 78241.030| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.26 r_work: 0.2920 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25782 Z= 0.203 Angle : 0.601 10.644 34979 Z= 0.295 Chirality : 0.045 0.142 3874 Planarity : 0.004 0.047 4484 Dihedral : 6.048 86.011 3594 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.04 % Allowed : 13.30 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 3157 helix: 1.11 (0.15), residues: 1323 sheet: 0.26 (0.20), residues: 618 loop : 0.48 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 372 TYR 0.010 0.001 TYR F 240 PHE 0.011 0.001 PHE H 255 TRP 0.019 0.002 TRP I 318 HIS 0.005 0.001 HIS I 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (25782) covalent geometry : angle 0.60080 / 0.29 (34979) hydrogen bonds : bond 0.03871 / 2.63 ( 1262) hydrogen bonds : angle 4.66040 / 3.28 ( 3237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2590 (pmm) cc_final: 0.2039 (pmm) REVERT: A 82 MET cc_start: 0.9608 (tpp) cc_final: 0.8883 (tpp) REVERT: A 86 TRP cc_start: 0.9133 (m-10) cc_final: 0.8882 (m-90) REVERT: A 107 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: A 123 MET cc_start: 0.9425 (tpp) cc_final: 0.9112 (tpp) REVERT: A 313 MET cc_start: 0.9524 (tpp) cc_final: 0.9314 (mmt) REVERT: A 355 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8595 (ttt) REVERT: B 82 MET cc_start: 0.9002 (tpt) cc_final: 0.8651 (tpp) REVERT: B 222 ASP cc_start: 0.8350 (t0) cc_final: 0.8067 (p0) REVERT: D 41 GLN cc_start: 0.8239 (mp10) cc_final: 0.7989 (tp40) REVERT: D 325 MET cc_start: 0.9056 (mmp) cc_final: 0.8782 (mmp) REVERT: D 361 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8047 (mt-10) REVERT: E 50 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8825 (tppt) REVERT: E 72 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8464 (pm20) REVERT: E 227 MET cc_start: 0.8700 (mmm) cc_final: 0.8380 (mmm) REVERT: E 345 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9175 (mp) REVERT: F 167 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8153 (tm-30) REVERT: F 227 MET cc_start: 0.8930 (mmm) cc_final: 0.8569 (mmm) REVERT: F 314 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.7933 (tp40) REVERT: G 82 MET cc_start: 0.8700 (tpt) cc_final: 0.8454 (tpt) REVERT: G 83 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8657 (pp20) REVERT: G 132 MET cc_start: 0.8958 (ppp) cc_final: 0.8662 (ppp) REVERT: G 176 MET cc_start: 0.8547 (mmt) cc_final: 0.8203 (mmm) REVERT: G 338 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.8970 (m) REVERT: H 176 MET cc_start: 0.8150 (mmt) cc_final: 0.7513 (mmm) REVERT: H 276 GLU cc_start: 0.9566 (mt-10) cc_final: 0.8981 (tp30) REVERT: H 305 MET cc_start: 0.9044 (tpp) cc_final: 0.8534 (mmt) REVERT: H 355 MET cc_start: 0.9458 (mtt) cc_final: 0.9241 (mpp) REVERT: I 189 PHE cc_start: 0.8581 (m-80) cc_final: 0.8307 (m-80) REVERT: I 270 LEU cc_start: 0.8949 (mt) cc_final: 0.8383 (mt) REVERT: I 274 TYR cc_start: 0.8185 (m-80) cc_final: 0.7844 (m-80) REVERT: I 283 MET cc_start: 0.6887 (tpp) cc_final: 0.6498 (tpp) REVERT: I 309 HIS cc_start: 0.8913 (t70) cc_final: 0.8093 (t70) REVERT: I 369 TRP cc_start: 0.7238 (t-100) cc_final: 0.5923 (t-100) outliers start: 55 outliers final: 42 residues processed: 223 average time/residue: 0.1494 time to fit residues: 56.9723 Evaluate side-chains 234 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 346 LYS Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 290 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 312 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 232 HIS ** 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 = 0.3497 r_free = 0.3497 target = 0.077024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056583 restraints weight = 77814.621| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.26 r_work: 0.2931 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25782 Z= 0.164 Angle : 0.578 10.273 34979 Z= 0.281 Chirality : 0.044 0.152 3874 Planarity : 0.004 0.046 4484 Dihedral : 5.875 82.285 3592 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.00 % Allowed : 13.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 3157 helix: 1.16 (0.15), residues: 1323 sheet: 0.35 (0.21), residues: 557 loop : 0.42 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 372 TYR 0.009 0.001 TYR A 337 PHE 0.012 0.001 PHE H 127 TRP 0.022 0.001 TRP I 318 HIS 0.004 0.001 HIS I 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (25782) covalent geometry : angle 0.57779 / 0.28 (34979) hydrogen bonds : bond 0.03539 / 2.41 ( 1262) hydrogen bonds : angle 4.58934 / 3.23 ( 3237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2542 (pmm) cc_final: 0.1968 (pmm) REVERT: A 82 MET cc_start: 0.9609 (tpp) cc_final: 0.8852 (tpp) REVERT: A 86 TRP cc_start: 0.9144 (m-10) cc_final: 0.8860 (m-90) REVERT: A 107 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: A 123 MET cc_start: 0.9437 (tpp) cc_final: 0.9094 (tpp) REVERT: A 313 MET cc_start: 0.9487 (tpp) cc_final: 0.9270 (mmt) REVERT: A 355 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8612 (ttt) REVERT: B 82 MET cc_start: 0.8998 (tpt) cc_final: 0.8565 (tpp) REVERT: B 222 ASP cc_start: 0.8346 (t0) cc_final: 0.8095 (p0) REVERT: D 361 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8033 (mt-10) REVERT: E 50 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8818 (tppt) REVERT: E 72 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8471 (pm20) REVERT: E 227 MET cc_start: 0.8734 (mmm) cc_final: 0.8394 (mmm) REVERT: E 345 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9176 (mp) REVERT: F 167 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8157 (tm-30) REVERT: F 227 MET cc_start: 0.8929 (mmm) cc_final: 0.8571 (mmm) REVERT: F 314 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7932 (tp40) REVERT: G 82 MET cc_start: 0.8645 (tpt) cc_final: 0.8397 (tpt) REVERT: G 83 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8645 (pp20) REVERT: G 132 MET cc_start: 0.8961 (ppp) cc_final: 0.8669 (ppp) REVERT: G 338 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8965 (m) REVERT: H 176 MET cc_start: 0.8130 (mmt) cc_final: 0.7493 (mmm) REVERT: H 276 GLU cc_start: 0.9569 (mt-10) cc_final: 0.8980 (tp30) REVERT: H 305 MET cc_start: 0.9033 (tpp) cc_final: 0.8507 (mmt) REVERT: H 372 ARG cc_start: 0.9012 (mtm-85) cc_final: 0.8681 (ptp-170) REVERT: I 189 PHE cc_start: 0.8529 (m-80) cc_final: 0.8293 (m-80) REVERT: I 243 MET cc_start: 0.8857 (ptp) cc_final: 0.8401 (tmm) REVERT: I 270 LEU cc_start: 0.9031 (mt) cc_final: 0.8531 (mt) REVERT: I 283 MET cc_start: 0.6671 (tpp) cc_final: 0.6117 (tpp) REVERT: I 309 HIS cc_start: 0.8843 (t70) cc_final: 0.8012 (t70) REVERT: I 369 TRP cc_start: 0.7260 (t-100) cc_final: 0.5865 (t-100) outliers start: 54 outliers final: 41 residues processed: 227 average time/residue: 0.1388 time to fit residues: 53.6950 Evaluate side-chains 232 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 346 LYS Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 152 optimal weight: 0.0870 chunk 273 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 255 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 GLN ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058523 restraints weight = 77229.757| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.30 r_work: 0.2977 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25782 Z= 0.091 Angle : 0.544 8.965 34979 Z= 0.260 Chirality : 0.042 0.171 3874 Planarity : 0.004 0.045 4484 Dihedral : 5.567 74.058 3592 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.26 % Allowed : 14.30 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.16), residues: 3157 helix: 1.30 (0.15), residues: 1321 sheet: 0.35 (0.21), residues: 618 loop : 0.60 (0.19), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 372 TYR 0.009 0.001 TYR B 143 PHE 0.015 0.001 PHE I 365 TRP 0.028 0.001 TRP I 318 HIS 0.004 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (25782) covalent geometry : angle 0.54356 / 0.26 (34979) hydrogen bonds : bond 0.02802 / 1.92 ( 1262) hydrogen bonds : angle 4.39728 / 3.08 ( 3237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2459 (pmm) cc_final: 0.1885 (pmm) REVERT: A 82 MET cc_start: 0.9607 (tpp) cc_final: 0.8824 (tpp) REVERT: A 86 TRP cc_start: 0.9129 (m-10) cc_final: 0.8815 (m-90) REVERT: A 123 MET cc_start: 0.9461 (tpp) cc_final: 0.9061 (tpp) REVERT: A 355 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8537 (ttt) REVERT: B 82 MET cc_start: 0.8995 (tpt) cc_final: 0.8575 (tpp) REVERT: B 222 ASP cc_start: 0.8318 (t0) cc_final: 0.8107 (p0) REVERT: C 132 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.7911 (tmm) REVERT: D 41 GLN cc_start: 0.8246 (mp10) cc_final: 0.7960 (tp40) REVERT: D 325 MET cc_start: 0.9090 (mmp) cc_final: 0.8824 (mmp) REVERT: D 361 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8053 (mt-10) REVERT: E 50 LYS cc_start: 0.9255 (mtmp) cc_final: 0.8713 (tppt) REVERT: E 227 MET cc_start: 0.8722 (mmm) cc_final: 0.8403 (mmm) REVERT: E 345 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9120 (mp) REVERT: F 167 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8220 (tm-30) REVERT: F 227 MET cc_start: 0.8903 (mmm) cc_final: 0.8541 (mmm) REVERT: F 314 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7887 (tp40) REVERT: G 82 MET cc_start: 0.8649 (tpt) cc_final: 0.8408 (tpt) REVERT: G 83 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8644 (pp20) REVERT: G 132 MET cc_start: 0.8935 (ppp) cc_final: 0.8633 (ppp) REVERT: G 338 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.8915 (m) REVERT: H 176 MET cc_start: 0.8009 (mmt) cc_final: 0.7357 (mmm) REVERT: H 276 GLU cc_start: 0.9562 (mt-10) cc_final: 0.8966 (tp30) REVERT: H 305 MET cc_start: 0.9014 (tpp) cc_final: 0.8322 (mmm) REVERT: I 165 VAL cc_start: 0.8482 (m) cc_final: 0.8220 (p) REVERT: I 189 PHE cc_start: 0.8380 (m-80) cc_final: 0.8069 (m-80) REVERT: I 270 LEU cc_start: 0.8964 (mt) cc_final: 0.8501 (mt) REVERT: I 283 MET cc_start: 0.6401 (tpp) cc_final: 0.5856 (tpp) REVERT: I 309 HIS cc_start: 0.8892 (t70) cc_final: 0.8185 (t70) REVERT: I 369 TRP cc_start: 0.7140 (t-100) cc_final: 0.5646 (t60) outliers start: 34 outliers final: 23 residues processed: 228 average time/residue: 0.1439 time to fit residues: 55.8314 Evaluate side-chains 218 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain I residue 346 LYS Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 57 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 265 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 242 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 208 optimal weight: 0.5980 chunk 287 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN F 162 ASN ** I 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.056361 restraints weight = 76710.607| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.23 r_work: 0.2918 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25782 Z= 0.127 Angle : 0.562 10.707 34979 Z= 0.270 Chirality : 0.043 0.145 3874 Planarity : 0.004 0.048 4484 Dihedral : 5.427 74.344 3583 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.22 % Allowed : 14.86 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.16), residues: 3157 helix: 1.32 (0.15), residues: 1320 sheet: 0.53 (0.21), residues: 569 loop : 0.53 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 372 TYR 0.007 0.001 TYR H 91 PHE 0.016 0.001 PHE I 365 TRP 0.030 0.001 TRP I 318 HIS 0.004 0.001 HIS I 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (25782) covalent geometry : angle 0.56212 / 0.27 (34979) hydrogen bonds : bond 0.03188 / 2.17 ( 1262) hydrogen bonds : angle 4.44311 / 3.11 ( 3237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5644.79 seconds wall clock time: 97 minutes 34.36 seconds (5854.36 seconds total)