Starting phenix.real_space_refine on Fri Feb 6 02:09:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zbl_73993/02_2026/9zbl_73993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zbl_73993/02_2026/9zbl_73993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zbl_73993/02_2026/9zbl_73993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zbl_73993/02_2026/9zbl_73993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zbl_73993/02_2026/9zbl_73993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zbl_73993/02_2026/9zbl_73993.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 132 5.16 5 C 13516 2.51 5 N 3656 2.21 5 O 4248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21570 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "B" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "M" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'TRANS': 123} Chain: "N" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'TRANS': 123} Chain: "O" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'TRANS': 123} Chain: "P" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1005 Classifications: {'peptide': 124} Link IDs: {'TRANS': 123} 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} Time building chain proxies: 5.07, per 1000 atoms: 0.24 Number of scatterers: 21570 At special positions: 0 Unit cell: (98.79, 103.24, 221.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 12 15.00 Mg 6 11.99 O 4248 8.00 N 3656 7.00 C 13516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5092 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 36 sheets defined 59.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.959A 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 195 removed outlier: 3.956A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.613A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) 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 284 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.738A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.671A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.833A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.998A 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 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.633A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.514A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.786A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.797A 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 368 through 374 removed outlier: 3.821A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) 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: 3.971A 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 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.621A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.762A 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 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.955A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.846A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.005A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 195 removed outlier: 4.056A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 222 through 232 removed outlier: 3.609A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.766A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.982A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 127 removed outlier: 4.013A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 222 through 232 removed outlier: 3.568A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 285 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.774A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.897A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.913A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.934A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 222 through 232 removed outlier: 3.616A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) 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 285 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.816A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.834A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 366 through 368 No H-bonds generated for 'chain 'F' and resid 366 through 368' Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'M' and resid 103 through 225 removed outlier: 3.794A pdb=" N ILE M 225 " --> pdb=" O TYR M 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 225 removed outlier: 3.594A pdb=" N ILE N 225 " --> pdb=" O TYR N 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 225 Processing helix chain 'P' and resid 103 through 225 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.691A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.423A 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 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.262A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (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: 6.680A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.460A 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 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.275A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (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: 4.209A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.150A 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 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.616A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (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: 6.702A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (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 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.564A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (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: 6.702A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.477A 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 removed outlier: 3.568A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) 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 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.655A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (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: 6.769A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (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 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.673A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 1372 hydrogen bonds defined for protein. 3708 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: 4.25 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7133 1.34 - 1.46: 3287 1.46 - 1.57: 11298 1.57 - 1.69: 18 1.69 - 1.81: 230 Bond restraints: 21966 Sorted by residual: bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" CB ASN C 162 " pdb=" CG ASN C 162 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.60e+00 ... (remaining 21961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 29325 2.48 - 4.95: 314 4.95 - 7.43: 61 7.43 - 9.90: 3 9.90 - 12.38: 1 Bond angle restraints: 29704 Sorted by residual: angle pdb=" CA ARG M 125 " pdb=" CB ARG M 125 " pdb=" CG ARG M 125 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CA ILE P 146 " pdb=" CB ILE P 146 " pdb=" CG1 ILE P 146 " ideal model delta sigma weight residual 110.40 116.97 -6.57 1.70e+00 3.46e-01 1.50e+01 angle pdb=" CA GLN O 147 " pdb=" CB GLN O 147 " pdb=" CG GLN O 147 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA ARG O 182 " pdb=" CB ARG O 182 " pdb=" CG ARG O 182 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 angle pdb=" C VAL O 170 " pdb=" N ILE O 171 " pdb=" CA ILE O 171 " ideal model delta sigma weight residual 120.30 114.40 5.90 1.64e+00 3.72e-01 1.29e+01 ... (remaining 29699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11300 17.84 - 35.67: 1441 35.67 - 53.51: 494 53.51 - 71.35: 128 71.35 - 89.18: 65 Dihedral angle restraints: 13428 sinusoidal: 5516 harmonic: 7912 Sorted by residual: dihedral pdb=" CA ASP A 80 " pdb=" CB ASP A 80 " pdb=" CG ASP A 80 " pdb=" OD1 ASP A 80 " ideal model delta sinusoidal sigma weight residual -30.00 -87.82 57.82 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP C 154 " pdb=" CB ASP C 154 " pdb=" CG ASP C 154 " pdb=" OD1 ASP C 154 " ideal model delta sinusoidal sigma weight residual -30.00 -86.88 56.88 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP D 80 " pdb=" CB ASP D 80 " pdb=" CG ASP D 80 " pdb=" OD1 ASP D 80 " ideal model delta sinusoidal sigma weight residual -30.00 -86.70 56.70 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 13425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2332 0.043 - 0.087: 700 0.087 - 0.130: 240 0.130 - 0.173: 18 0.173 - 0.217: 4 Chirality restraints: 3294 Sorted by residual: chirality pdb=" CB THR P 201 " pdb=" CA THR P 201 " pdb=" OG1 THR P 201 " pdb=" CG2 THR P 201 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR O 201 " pdb=" CA THR O 201 " pdb=" OG1 THR O 201 " pdb=" CG2 THR O 201 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA TYR N 214 " pdb=" N TYR N 214 " pdb=" C TYR N 214 " pdb=" CB TYR N 214 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 3291 not shown) Planarity restraints: 3832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 221 " 0.011 2.00e-02 2.50e+03 1.38e-02 3.82e+00 pdb=" CG TYR O 221 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR O 221 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR O 221 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR O 221 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR O 221 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR O 221 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR O 221 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 214 " 0.011 2.00e-02 2.50e+03 1.26e-02 3.16e+00 pdb=" CG TYR N 214 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR N 214 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR N 214 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR N 214 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR N 214 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR N 214 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP P 121 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" CG ASP P 121 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP P 121 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP P 121 " 0.010 2.00e-02 2.50e+03 ... (remaining 3829 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 38 2.59 - 3.17: 18472 3.17 - 3.75: 35060 3.75 - 4.32: 48709 4.32 - 4.90: 80969 Nonbonded interactions: 183248 Sorted by model distance: nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.014 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.036 2.170 nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.041 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.138 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.158 2.170 ... (remaining 183243 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.820 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 21966 Z= 0.238 Angle : 0.625 12.381 29704 Z= 0.316 Chirality : 0.046 0.217 3294 Planarity : 0.003 0.062 3832 Dihedral : 19.053 89.182 8336 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.34 % Allowed : 29.77 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.97 (0.17), residues: 2702 helix: 1.71 (0.14), residues: 1374 sheet: 0.49 (0.26), residues: 402 loop : 1.31 (0.22), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG P 160 TYR 0.034 0.001 TYR O 221 PHE 0.008 0.001 PHE C 255 TRP 0.009 0.002 TRP C 79 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00550 (21966) covalent geometry : angle 0.62527 (29704) hydrogen bonds : bond 0.11701 ( 1360) hydrogen bonds : angle 5.18892 ( 3708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 185 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8198 (pp20) REVERT: A 176 MET cc_start: 0.8792 (mtp) cc_final: 0.8449 (mtt) REVERT: A 217 CYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8559 (m) REVERT: B 47 MET cc_start: 0.7817 (ttp) cc_final: 0.7526 (ptm) REVERT: C 47 MET cc_start: 0.7724 (ttp) cc_final: 0.7497 (ttt) REVERT: C 286 ASP cc_start: 0.9017 (t0) cc_final: 0.8441 (m-30) REVERT: D 286 ASP cc_start: 0.8892 (t0) cc_final: 0.8141 (m-30) REVERT: E 286 ASP cc_start: 0.8941 (t0) cc_final: 0.8429 (m-30) REVERT: F 44 MET cc_start: 0.9413 (tpp) cc_final: 0.9160 (mmm) REVERT: F 113 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8255 (mmmm) REVERT: F 162 ASN cc_start: 0.9026 (t0) cc_final: 0.8676 (t0) REVERT: M 121 ASP cc_start: 0.9258 (p0) cc_final: 0.9011 (m-30) REVERT: M 127 MET cc_start: 0.7548 (tpp) cc_final: 0.7276 (tpt) REVERT: M 165 VAL cc_start: 0.8051 (t) cc_final: 0.7791 (m) REVERT: N 153 HIS cc_start: 0.9597 (OUTLIER) cc_final: 0.9256 (p90) REVERT: O 159 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7962 (p0) REVERT: P 127 MET cc_start: 0.8435 (tpt) cc_final: 0.8173 (mmm) REVERT: P 141 MET cc_start: 0.9291 (tpt) cc_final: 0.9014 (mmm) outliers start: 54 outliers final: 35 residues processed: 225 average time/residue: 0.6268 time to fit residues: 161.4409 Evaluate side-chains 222 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 159 ASP Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 162 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN F 297 ASN ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.046816 restraints weight = 49944.913| |-----------------------------------------------------------------------------| r_work (start): 0.2599 rms_B_bonded: 2.51 r_work: 0.2446 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2310 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21966 Z= 0.144 Angle : 0.558 9.225 29704 Z= 0.279 Chirality : 0.043 0.153 3294 Planarity : 0.003 0.046 3832 Dihedral : 6.465 59.583 3099 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.72 % Allowed : 26.43 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.17), residues: 2702 helix: 1.84 (0.14), residues: 1368 sheet: 0.62 (0.26), residues: 390 loop : 1.22 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 160 TYR 0.019 0.001 TYR M 214 PHE 0.007 0.001 PHE E 127 TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00315 (21966) covalent geometry : angle 0.55774 (29704) hydrogen bonds : bond 0.04700 ( 1360) hydrogen bonds : angle 4.44280 ( 3708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 196 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8777 (mtp) cc_final: 0.8444 (mtt) REVERT: B 47 MET cc_start: 0.7777 (ttp) cc_final: 0.7476 (ptm) REVERT: B 162 ASN cc_start: 0.9071 (t0) cc_final: 0.8756 (t0) REVERT: B 176 MET cc_start: 0.9094 (mtp) cc_final: 0.8703 (mtm) REVERT: C 180 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8949 (pt) REVERT: F 162 ASN cc_start: 0.8985 (t0) cc_final: 0.8714 (t0) REVERT: F 314 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8824 (tt0) REVERT: M 127 MET cc_start: 0.7476 (tpp) cc_final: 0.7074 (tpt) REVERT: M 130 ILE cc_start: 0.8778 (tt) cc_final: 0.8545 (tt) REVERT: M 165 VAL cc_start: 0.8038 (t) cc_final: 0.7775 (m) REVERT: N 127 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7511 (tpt) REVERT: N 144 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: N 153 HIS cc_start: 0.9616 (OUTLIER) cc_final: 0.9277 (p90) REVERT: O 159 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8101 (p0) REVERT: P 127 MET cc_start: 0.8469 (tpt) cc_final: 0.8199 (mmm) REVERT: P 190 CYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6550 (p) outliers start: 109 outliers final: 36 residues processed: 281 average time/residue: 0.6112 time to fit residues: 196.6579 Evaluate side-chains 230 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 127 MET Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 159 ASP Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 190 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 142 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 261 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 219 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 297 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.046914 restraints weight = 50029.033| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.51 r_work: 0.2452 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21966 Z= 0.141 Angle : 0.552 7.717 29704 Z= 0.275 Chirality : 0.043 0.164 3294 Planarity : 0.003 0.029 3832 Dihedral : 5.757 58.286 3058 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.07 % Allowed : 26.82 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.17), residues: 2702 helix: 1.88 (0.14), residues: 1368 sheet: 0.65 (0.26), residues: 390 loop : 1.15 (0.22), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 160 TYR 0.028 0.001 TYR O 221 PHE 0.006 0.001 PHE F 255 TRP 0.009 0.001 TRP C 79 HIS 0.006 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00310 (21966) covalent geometry : angle 0.55228 (29704) hydrogen bonds : bond 0.04547 ( 1360) hydrogen bonds : angle 4.31059 ( 3708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 201 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8770 (mtp) cc_final: 0.8441 (mtt) REVERT: A 217 CYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8485 (m) REVERT: B 47 MET cc_start: 0.7812 (ttp) cc_final: 0.7466 (ptm) REVERT: B 162 ASN cc_start: 0.9067 (t0) cc_final: 0.8742 (t0) REVERT: C 65 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8672 (pp) REVERT: D 6 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8869 (t) REVERT: D 328 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8682 (ttmm) REVERT: E 6 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8949 (t) REVERT: F 6 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8726 (t) REVERT: F 44 MET cc_start: 0.9474 (tpp) cc_final: 0.9222 (mmm) REVERT: F 162 ASN cc_start: 0.8986 (t0) cc_final: 0.8731 (t0) REVERT: F 314 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: F 328 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: M 127 MET cc_start: 0.7502 (tpp) cc_final: 0.7172 (tpt) REVERT: M 165 VAL cc_start: 0.8048 (t) cc_final: 0.7789 (m) REVERT: N 144 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: N 153 HIS cc_start: 0.9615 (OUTLIER) cc_final: 0.9267 (p90) REVERT: O 157 ASP cc_start: 0.9059 (p0) cc_final: 0.8821 (p0) REVERT: O 159 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8185 (p0) REVERT: P 127 MET cc_start: 0.8470 (tpt) cc_final: 0.8209 (mmm) REVERT: P 176 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.4270 (mm) outliers start: 94 outliers final: 35 residues processed: 272 average time/residue: 0.5672 time to fit residues: 177.9345 Evaluate side-chains 235 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 160 ARG Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 159 ASP Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 176 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 124 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 257 optimal weight: 30.0000 chunk 142 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 266 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 297 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 203 ASN ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.080502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.046173 restraints weight = 50363.147| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 2.51 r_work: 0.2433 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2297 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.0568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21966 Z= 0.192 Angle : 0.579 9.191 29704 Z= 0.289 Chirality : 0.044 0.179 3294 Planarity : 0.003 0.040 3832 Dihedral : 5.668 58.934 3049 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.20 % Allowed : 25.91 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.16), residues: 2702 helix: 1.85 (0.14), residues: 1362 sheet: 0.63 (0.25), residues: 390 loop : 1.11 (0.22), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 133 TYR 0.017 0.001 TYR M 214 PHE 0.006 0.001 PHE C 255 TRP 0.010 0.001 TRP C 79 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00442 (21966) covalent geometry : angle 0.57906 (29704) hydrogen bonds : bond 0.04629 ( 1360) hydrogen bonds : angle 4.30197 ( 3708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 191 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8773 (mtp) cc_final: 0.8441 (mtt) REVERT: A 217 CYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8539 (m) REVERT: B 47 MET cc_start: 0.7841 (ttp) cc_final: 0.7460 (ptm) REVERT: C 6 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8923 (t) REVERT: C 65 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8690 (pp) REVERT: C 180 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8953 (pt) REVERT: D 6 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8851 (t) REVERT: D 328 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8669 (ttmm) REVERT: E 6 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8929 (t) REVERT: E 355 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.9273 (mtm) REVERT: F 6 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8717 (t) REVERT: F 44 MET cc_start: 0.9457 (tpp) cc_final: 0.9204 (mmm) REVERT: F 162 ASN cc_start: 0.9000 (t0) cc_final: 0.8720 (t0) REVERT: F 314 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8811 (tt0) REVERT: F 328 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8391 (ttmm) REVERT: M 127 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7067 (tpt) REVERT: M 165 VAL cc_start: 0.8055 (t) cc_final: 0.7799 (m) REVERT: N 123 SER cc_start: 0.8106 (m) cc_final: 0.7746 (m) REVERT: N 127 MET cc_start: 0.7671 (tpt) cc_final: 0.7385 (tpt) REVERT: N 144 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: N 153 HIS cc_start: 0.9614 (OUTLIER) cc_final: 0.9290 (p90) REVERT: N 190 CYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7301 (p) REVERT: P 127 MET cc_start: 0.8440 (tpt) cc_final: 0.8170 (mmm) REVERT: P 141 MET cc_start: 0.9272 (tpt) cc_final: 0.8900 (mmm) REVERT: P 176 LEU cc_start: 0.4602 (OUTLIER) cc_final: 0.4331 (mm) REVERT: P 190 CYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6645 (p) outliers start: 120 outliers final: 61 residues processed: 286 average time/residue: 0.5840 time to fit residues: 192.5324 Evaluate side-chains 262 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 184 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 160 ARG Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 159 ASP Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 190 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 127 optimal weight: 1.9990 chunk 113 optimal weight: 0.0030 chunk 14 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 297 ASN O 147 GLN ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.047504 restraints weight = 49945.073| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 2.45 r_work: 0.2452 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2316 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21966 Z= 0.141 Angle : 0.567 7.519 29704 Z= 0.282 Chirality : 0.043 0.205 3294 Planarity : 0.003 0.031 3832 Dihedral : 5.605 59.354 3049 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.64 % Allowed : 26.43 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.16), residues: 2702 helix: 1.89 (0.14), residues: 1362 sheet: 0.63 (0.25), residues: 390 loop : 1.13 (0.22), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 160 TYR 0.031 0.001 TYR O 221 PHE 0.006 0.001 PHE D 255 TRP 0.010 0.001 TRP D 79 HIS 0.005 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00313 (21966) covalent geometry : angle 0.56660 (29704) hydrogen bonds : bond 0.04476 ( 1360) hydrogen bonds : angle 4.23277 ( 3708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 198 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8748 (mtp) cc_final: 0.8411 (mtt) REVERT: A 217 CYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 47 MET cc_start: 0.7782 (ttp) cc_final: 0.7391 (ptm) REVERT: B 162 ASN cc_start: 0.9045 (t0) cc_final: 0.8732 (t0) REVERT: D 6 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8838 (t) REVERT: D 328 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8615 (ttmm) REVERT: E 6 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8923 (t) REVERT: E 355 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9247 (mtm) REVERT: F 6 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8715 (t) REVERT: F 44 MET cc_start: 0.9461 (tpp) cc_final: 0.9210 (mmm) REVERT: F 162 ASN cc_start: 0.8970 (t0) cc_final: 0.8716 (t0) REVERT: F 314 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: F 328 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8348 (ttmm) REVERT: M 127 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6895 (tpt) REVERT: M 165 VAL cc_start: 0.8054 (t) cc_final: 0.7794 (m) REVERT: N 123 SER cc_start: 0.8119 (m) cc_final: 0.7735 (m) REVERT: N 127 MET cc_start: 0.7698 (tpt) cc_final: 0.7286 (tpt) REVERT: N 144 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: N 153 HIS cc_start: 0.9632 (OUTLIER) cc_final: 0.9280 (p90) REVERT: N 190 CYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7319 (p) REVERT: P 123 SER cc_start: 0.8589 (m) cc_final: 0.7813 (p) REVERT: P 127 MET cc_start: 0.8441 (tpt) cc_final: 0.8181 (mmm) REVERT: P 176 LEU cc_start: 0.4605 (OUTLIER) cc_final: 0.4331 (mm) REVERT: P 190 CYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6668 (p) outliers start: 107 outliers final: 58 residues processed: 281 average time/residue: 0.5937 time to fit residues: 192.2136 Evaluate side-chains 261 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 189 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 160 ARG Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 140 LYS Chi-restraints excluded: chain O residue 159 ASP Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 190 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 61 optimal weight: 5.9990 chunk 219 optimal weight: 0.0870 chunk 66 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 235 optimal weight: 40.0000 chunk 175 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 224 optimal weight: 30.0000 chunk 197 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 297 ASN N 203 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.080522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.046237 restraints weight = 50248.227| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 2.51 r_work: 0.2431 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2296 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21966 Z= 0.182 Angle : 0.579 7.489 29704 Z= 0.289 Chirality : 0.044 0.208 3294 Planarity : 0.003 0.036 3832 Dihedral : 5.644 59.969 3049 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.16 % Allowed : 26.56 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.16), residues: 2702 helix: 1.89 (0.14), residues: 1362 sheet: 0.60 (0.25), residues: 390 loop : 1.10 (0.22), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 125 TYR 0.019 0.001 TYR M 214 PHE 0.006 0.001 PHE C 255 TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00418 (21966) covalent geometry : angle 0.57920 (29704) hydrogen bonds : bond 0.04585 ( 1360) hydrogen bonds : angle 4.24847 ( 3708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 191 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8764 (mtp) cc_final: 0.8425 (mtt) REVERT: A 217 CYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8540 (m) REVERT: C 65 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8694 (pp) REVERT: C 180 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.8978 (pt) REVERT: D 6 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8850 (t) REVERT: D 328 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8653 (ttmm) REVERT: E 6 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8925 (t) REVERT: F 6 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8724 (t) REVERT: F 44 MET cc_start: 0.9454 (tpp) cc_final: 0.9211 (mmm) REVERT: F 162 ASN cc_start: 0.9004 (t0) cc_final: 0.8737 (t0) REVERT: F 314 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8804 (tt0) REVERT: F 328 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8375 (ttmm) REVERT: M 127 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7075 (tpt) REVERT: M 165 VAL cc_start: 0.8055 (t) cc_final: 0.7806 (m) REVERT: N 123 SER cc_start: 0.8150 (m) cc_final: 0.7793 (m) REVERT: N 127 MET cc_start: 0.7796 (tpt) cc_final: 0.7503 (tpt) REVERT: N 144 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: N 153 HIS cc_start: 0.9627 (OUTLIER) cc_final: 0.9279 (p90) REVERT: N 190 CYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7318 (p) REVERT: P 123 SER cc_start: 0.8574 (m) cc_final: 0.7711 (p) REVERT: P 127 MET cc_start: 0.8394 (tpt) cc_final: 0.8113 (mmm) REVERT: P 176 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4364 (mm) REVERT: P 190 CYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6701 (p) outliers start: 119 outliers final: 63 residues processed: 283 average time/residue: 0.5851 time to fit residues: 190.5156 Evaluate side-chains 262 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 184 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 160 ARG Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 159 ASP Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 190 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 262 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 142 optimal weight: 0.0870 chunk 168 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.0870 chunk 62 optimal weight: 0.6980 chunk 208 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 297 ASN N 203 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.082431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.048233 restraints weight = 49518.903| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 2.52 r_work: 0.2491 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2356 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 21966 Z= 0.107 Angle : 0.564 7.550 29704 Z= 0.282 Chirality : 0.042 0.199 3294 Planarity : 0.003 0.040 3832 Dihedral : 5.502 59.854 3049 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.99 % Allowed : 28.60 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.16), residues: 2702 helix: 1.76 (0.14), residues: 1398 sheet: 0.67 (0.26), residues: 390 loop : 1.13 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG M 125 TYR 0.036 0.001 TYR N 214 PHE 0.006 0.001 PHE D 255 TRP 0.009 0.001 TRP D 79 HIS 0.006 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00208 (21966) covalent geometry : angle 0.56428 (29704) hydrogen bonds : bond 0.04277 ( 1360) hydrogen bonds : angle 4.14734 ( 3708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 202 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8738 (mtp) cc_final: 0.8401 (mtt) REVERT: A 217 CYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8408 (m) REVERT: B 162 ASN cc_start: 0.8989 (t0) cc_final: 0.8737 (t0) REVERT: D 328 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8678 (ttmm) REVERT: E 355 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.9196 (mtm) REVERT: F 44 MET cc_start: 0.9457 (tpp) cc_final: 0.9219 (mmm) REVERT: F 162 ASN cc_start: 0.8898 (t0) cc_final: 0.8680 (t0) REVERT: F 328 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8305 (ttmm) REVERT: M 127 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7065 (tpt) REVERT: M 165 VAL cc_start: 0.8098 (t) cc_final: 0.7837 (m) REVERT: N 123 SER cc_start: 0.8206 (m) cc_final: 0.7853 (m) REVERT: N 127 MET cc_start: 0.7974 (tpt) cc_final: 0.7700 (tpt) REVERT: N 144 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8681 (tt0) REVERT: N 153 HIS cc_start: 0.9624 (OUTLIER) cc_final: 0.9264 (p90) REVERT: N 190 CYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7333 (p) REVERT: P 141 MET cc_start: 0.9396 (tpt) cc_final: 0.9152 (mmm) REVERT: P 176 LEU cc_start: 0.4668 (OUTLIER) cc_final: 0.4406 (mm) REVERT: P 190 CYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6765 (p) outliers start: 69 outliers final: 38 residues processed: 253 average time/residue: 0.5416 time to fit residues: 157.1718 Evaluate side-chains 239 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 159 ASP Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 190 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 23 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 297 ASN ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.082348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.048691 restraints weight = 49673.590| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 2.46 r_work: 0.2490 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2354 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 21966 Z= 0.115 Angle : 0.567 8.701 29704 Z= 0.283 Chirality : 0.043 0.205 3294 Planarity : 0.003 0.060 3832 Dihedral : 5.460 59.789 3043 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.34 % Allowed : 28.25 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.16), residues: 2702 helix: 1.79 (0.14), residues: 1400 sheet: 0.71 (0.26), residues: 390 loop : 1.15 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG P 160 TYR 0.020 0.001 TYR M 214 PHE 0.006 0.001 PHE C 255 TRP 0.009 0.001 TRP D 79 HIS 0.005 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00239 (21966) covalent geometry : angle 0.56671 (29704) hydrogen bonds : bond 0.04299 ( 1360) hydrogen bonds : angle 4.12489 ( 3708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 193 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8719 (mtp) cc_final: 0.8380 (mtt) REVERT: A 217 CYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8434 (m) REVERT: B 162 ASN cc_start: 0.9011 (t0) cc_final: 0.8750 (t0) REVERT: C 65 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8674 (pp) REVERT: D 328 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8629 (ttmm) REVERT: E 95 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8885 (mtp85) REVERT: E 355 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.9206 (mtm) REVERT: F 44 MET cc_start: 0.9452 (tpp) cc_final: 0.9224 (mmm) REVERT: F 162 ASN cc_start: 0.8909 (t0) cc_final: 0.8681 (t0) REVERT: F 314 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: F 328 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8296 (ttmm) REVERT: M 127 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7043 (tpt) REVERT: M 165 VAL cc_start: 0.8064 (t) cc_final: 0.7813 (m) REVERT: N 123 SER cc_start: 0.8218 (m) cc_final: 0.7869 (m) REVERT: N 127 MET cc_start: 0.8045 (tpt) cc_final: 0.7782 (tpt) REVERT: N 144 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8694 (tt0) REVERT: N 153 HIS cc_start: 0.9622 (OUTLIER) cc_final: 0.9262 (p90) REVERT: N 190 CYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7357 (p) REVERT: P 127 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7259 (mmm) REVERT: P 176 LEU cc_start: 0.4580 (OUTLIER) cc_final: 0.4301 (mm) REVERT: P 190 CYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6794 (p) outliers start: 77 outliers final: 47 residues processed: 246 average time/residue: 0.5774 time to fit residues: 163.1536 Evaluate side-chains 248 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 190 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 189 optimal weight: 0.0030 chunk 89 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 265 optimal weight: 40.0000 chunk 61 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 297 ASN ** P 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.049013 restraints weight = 49934.499| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 2.49 r_work: 0.2497 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2362 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 21966 Z= 0.112 Angle : 0.571 9.314 29704 Z= 0.286 Chirality : 0.043 0.214 3294 Planarity : 0.003 0.064 3832 Dihedral : 5.429 59.312 3043 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 3.08 % Allowed : 28.51 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.16), residues: 2702 helix: 1.81 (0.14), residues: 1400 sheet: 0.72 (0.26), residues: 390 loop : 1.18 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG M 125 TYR 0.035 0.001 TYR O 221 PHE 0.006 0.001 PHE C 255 TRP 0.009 0.001 TRP D 79 HIS 0.006 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00229 (21966) covalent geometry : angle 0.57124 (29704) hydrogen bonds : bond 0.04256 ( 1360) hydrogen bonds : angle 4.11261 ( 3708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 194 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8712 (mtp) cc_final: 0.8372 (mtt) REVERT: A 217 CYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8410 (m) REVERT: B 162 ASN cc_start: 0.8998 (t0) cc_final: 0.8750 (t0) REVERT: C 65 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8653 (pp) REVERT: D 328 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8675 (ttmm) REVERT: E 95 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8894 (mtp85) REVERT: E 355 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.9194 (mtm) REVERT: F 162 ASN cc_start: 0.8899 (t0) cc_final: 0.8681 (t0) REVERT: F 314 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8692 (tt0) REVERT: F 328 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8287 (ttmm) REVERT: M 105 ARG cc_start: 0.9059 (tmt-80) cc_final: 0.8787 (ptm-80) REVERT: M 127 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7098 (tpt) REVERT: M 165 VAL cc_start: 0.8093 (t) cc_final: 0.7841 (m) REVERT: N 123 SER cc_start: 0.8340 (m) cc_final: 0.7997 (m) REVERT: N 127 MET cc_start: 0.8108 (tpt) cc_final: 0.7862 (tpt) REVERT: N 144 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8727 (tt0) REVERT: N 153 HIS cc_start: 0.9620 (OUTLIER) cc_final: 0.9259 (p90) REVERT: N 190 CYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7369 (p) REVERT: O 157 ASP cc_start: 0.8985 (p0) cc_final: 0.8778 (p0) REVERT: P 127 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7496 (mmm) REVERT: P 141 MET cc_start: 0.9376 (tpt) cc_final: 0.9065 (mmm) REVERT: P 176 LEU cc_start: 0.4600 (OUTLIER) cc_final: 0.4326 (mm) REVERT: P 190 CYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6822 (p) outliers start: 71 outliers final: 44 residues processed: 243 average time/residue: 0.6011 time to fit residues: 167.1924 Evaluate side-chains 243 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 190 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 122 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 297 ASN ** O 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.082441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.048616 restraints weight = 49609.020| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 2.49 r_work: 0.2491 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2356 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21966 Z= 0.124 Angle : 0.593 11.238 29704 Z= 0.297 Chirality : 0.043 0.216 3294 Planarity : 0.003 0.066 3832 Dihedral : 5.373 59.008 3040 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.92 % Favored : 98.04 % Rotamer: Outliers : 2.69 % Allowed : 28.90 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.16), residues: 2702 helix: 1.79 (0.14), residues: 1406 sheet: 0.72 (0.26), residues: 390 loop : 1.17 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG M 125 TYR 0.021 0.001 TYR M 214 PHE 0.007 0.001 PHE C 255 TRP 0.009 0.001 TRP D 79 HIS 0.007 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00265 (21966) covalent geometry : angle 0.59304 (29704) hydrogen bonds : bond 0.04294 ( 1360) hydrogen bonds : angle 4.13486 ( 3708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8717 (mtp) cc_final: 0.8374 (mtt) REVERT: A 217 CYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8431 (m) REVERT: B 162 ASN cc_start: 0.9023 (t0) cc_final: 0.8771 (t0) REVERT: C 65 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8671 (pp) REVERT: D 328 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8672 (ttmm) REVERT: E 95 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8885 (mtp85) REVERT: E 355 MET cc_start: 0.9464 (OUTLIER) cc_final: 0.9184 (mtm) REVERT: F 162 ASN cc_start: 0.8926 (t0) cc_final: 0.8686 (t0) REVERT: F 314 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: F 328 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8295 (ttmm) REVERT: M 127 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7117 (tpt) REVERT: M 165 VAL cc_start: 0.8105 (t) cc_final: 0.7853 (m) REVERT: N 123 SER cc_start: 0.8368 (m) cc_final: 0.8074 (m) REVERT: N 127 MET cc_start: 0.8172 (tpt) cc_final: 0.7935 (tpt) REVERT: N 144 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: N 153 HIS cc_start: 0.9618 (OUTLIER) cc_final: 0.9372 (p-80) REVERT: N 190 CYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7378 (p) REVERT: P 127 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7182 (mmm) REVERT: P 141 MET cc_start: 0.9376 (tpt) cc_final: 0.9126 (mmm) REVERT: P 176 LEU cc_start: 0.4587 (OUTLIER) cc_final: 0.4317 (mm) REVERT: P 190 CYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6849 (p) outliers start: 62 outliers final: 46 residues processed: 233 average time/residue: 0.6173 time to fit residues: 164.0145 Evaluate side-chains 246 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 359 LYS Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 144 GLN Chi-restraints excluded: chain N residue 153 HIS Chi-restraints excluded: chain N residue 190 CYS Chi-restraints excluded: chain N residue 221 TYR Chi-restraints excluded: chain O residue 105 ARG Chi-restraints excluded: chain O residue 194 GLU Chi-restraints excluded: chain P residue 127 MET Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 162 TYR Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 190 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 258 optimal weight: 7.9990 chunk 60 optimal weight: 0.0070 chunk 217 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 178 optimal weight: 0.0050 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 297 ASN D 297 ASN E 297 ASN F 173 HIS F 297 ASN ** O 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.049284 restraints weight = 50012.158| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 2.50 r_work: 0.2507 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2372 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 21966 Z= 0.111 Angle : 0.593 11.632 29704 Z= 0.298 Chirality : 0.043 0.215 3294 Planarity : 0.003 0.064 3832 Dihedral : 5.347 58.262 3040 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 28.90 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.17), residues: 2702 helix: 1.97 (0.14), residues: 1364 sheet: 0.76 (0.26), residues: 390 loop : 1.27 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG M 125 TYR 0.035 0.001 TYR O 221 PHE 0.006 0.001 PHE C 255 TRP 0.009 0.001 TRP D 79 HIS 0.008 0.001 HIS P 153 Details of bonding type rmsd covalent geometry : bond 0.00223 (21966) covalent geometry : angle 0.59259 (29704) hydrogen bonds : bond 0.04209 ( 1360) hydrogen bonds : angle 4.10736 ( 3708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8702.65 seconds wall clock time: 148 minutes 49.45 seconds (8929.45 seconds total)