Starting phenix.real_space_refine on Wed Apr 8 20:31:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r61_53599/04_2026/9r61_53599_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r61_53599/04_2026/9r61_53599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r61_53599/04_2026/9r61_53599_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r61_53599/04_2026/9r61_53599_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r61_53599/04_2026/9r61_53599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r61_53599/04_2026/9r61_53599.map" } resolution = 2.7 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= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 104 5.16 5 C 13568 2.51 5 N 3776 2.21 5 O 4168 1.98 5 H 21584 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43200 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5400 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Chain: "B" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5400 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Chain: "C" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5400 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Chain: "D" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5400 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Chain: "E" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5400 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Chain: "F" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5400 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Chain: "G" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5400 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Chain: "H" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 5400 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 19, 'TRANS': 328} Time building chain proxies: 7.37, per 1000 atoms: 0.17 Number of scatterers: 43200 At special positions: 0 Unit cell: (119.21, 117.39, 140.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 O 4168 8.00 N 3776 7.00 C 13568 6.00 H 21584 1.00 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: 3.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 32 sheets defined 32.5% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 45 through 48 Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 140 through 153 removed outlier: 3.507A pdb=" N ALA A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.155A pdb=" N ASP A 254 " --> pdb=" O ARG A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.614A pdb=" N ALA A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.961A pdb=" N GLN A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'B' and resid 45 through 48 Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.940A pdb=" N GLY B 117 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 153 removed outlier: 3.500A pdb=" N ALA B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 251 through 254 removed outlier: 4.154A pdb=" N ASP B 254 " --> pdb=" O ARG B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 277 through 285 Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.805A pdb=" N ARG B 310 " --> pdb=" O GLU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.679A pdb=" N ALA B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 359 through 369 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'C' and resid 56 through 64 Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 140 through 153 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 251 through 254 removed outlier: 4.010A pdb=" N ASP C 254 " --> pdb=" O ARG C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 254' Processing helix chain 'C' and resid 277 through 285 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.640A pdb=" N ALA C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.999A pdb=" N GLN C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 369 removed outlier: 3.525A pdb=" N ILE C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 56 through 64 Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.511A pdb=" N ASN D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 140 through 153 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 251 through 254 removed outlier: 4.052A pdb=" N ASP D 254 " --> pdb=" O ARG D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 254' Processing helix chain 'D' and resid 277 through 285 Processing helix chain 'D' and resid 306 through 311 removed outlier: 3.928A pdb=" N GLY D 309 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG D 310 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.634A pdb=" N ALA D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 358 removed outlier: 3.999A pdb=" N GLN D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 369 Processing helix chain 'E' and resid 45 through 48 Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 73 through 82 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 140 through 153 Processing helix chain 'E' and resid 193 through 201 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 251 through 254 removed outlier: 4.196A pdb=" N ASP E 254 " --> pdb=" O ARG E 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 251 through 254' Processing helix chain 'E' and resid 277 through 285 Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 327 through 332 removed outlier: 3.618A pdb=" N ALA E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 357 Processing helix chain 'E' and resid 359 through 369 removed outlier: 3.505A pdb=" N ILE E 363 " --> pdb=" O LEU E 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 48 Processing helix chain 'F' and resid 56 through 64 Processing helix chain 'F' and resid 73 through 82 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 140 through 153 Processing helix chain 'F' and resid 193 through 201 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 251 through 254 removed outlier: 4.019A pdb=" N ASP F 254 " --> pdb=" O ARG F 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 251 through 254' Processing helix chain 'F' and resid 277 through 285 Processing helix chain 'F' and resid 324 through 326 No H-bonds generated for 'chain 'F' and resid 324 through 326' Processing helix chain 'F' and resid 327 through 332 removed outlier: 3.621A pdb=" N ALA F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 358 removed outlier: 4.002A pdb=" N GLN F 358 " --> pdb=" O ARG F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 369 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.502A pdb=" N LYS G 48 " --> pdb=" O ASP G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 56 through 64 Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 140 through 153 removed outlier: 3.502A pdb=" N ALA G 153 " --> pdb=" O THR G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 201 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 251 through 254 removed outlier: 4.182A pdb=" N ASP G 254 " --> pdb=" O ARG G 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 251 through 254' Processing helix chain 'G' and resid 277 through 285 Processing helix chain 'G' and resid 324 through 326 No H-bonds generated for 'chain 'G' and resid 324 through 326' Processing helix chain 'G' and resid 327 through 332 removed outlier: 3.609A pdb=" N ALA G 331 " --> pdb=" O SER G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 357 Processing helix chain 'G' and resid 359 through 369 Processing helix chain 'H' and resid 45 through 48 Processing helix chain 'H' and resid 56 through 64 Processing helix chain 'H' and resid 73 through 82 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 140 through 153 Processing helix chain 'H' and resid 193 through 201 Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 234 through 238 Processing helix chain 'H' and resid 251 through 254 removed outlier: 3.971A pdb=" N ASP H 254 " --> pdb=" O ARG H 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 251 through 254' Processing helix chain 'H' and resid 277 through 285 Processing helix chain 'H' and resid 306 through 311 Processing helix chain 'H' and resid 324 through 326 No H-bonds generated for 'chain 'H' and resid 324 through 326' Processing helix chain 'H' and resid 327 through 332 removed outlier: 3.655A pdb=" N ALA H 331 " --> pdb=" O SER H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 358 removed outlier: 4.002A pdb=" N GLN H 358 " --> pdb=" O ARG H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.921A pdb=" N ASP A 35 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 298 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY C 297 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS C 256 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N VAL C 342 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE C 258 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL C 344 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET C 260 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR C 346 " --> pdb=" O MET C 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 270 removed outlier: 7.493A pdb=" N LYS A 256 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N VAL A 342 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 258 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL A 344 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N MET A 260 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N THR A 346 " --> pdb=" O MET A 260 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY A 297 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 298 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP D 35 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.578A pdb=" N VAL A 92 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 128 Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 186 removed outlier: 9.203A pdb=" N LEU A 247 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 174 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL A 249 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER A 176 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.889A pdb=" N ASP B 35 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE H 298 " --> pdb=" O LEU H 320 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY H 297 " --> pdb=" O THR H 345 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LYS H 256 " --> pdb=" O ASP H 340 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N VAL H 342 " --> pdb=" O LYS H 256 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE H 258 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL H 344 " --> pdb=" O PHE H 258 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET H 260 " --> pdb=" O VAL H 344 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N THR H 346 " --> pdb=" O MET H 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 267 through 270 removed outlier: 7.494A pdb=" N LYS B 256 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N VAL B 342 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE B 258 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL B 344 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET B 260 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 346 " --> pdb=" O MET B 260 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY B 297 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 298 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP C 35 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.587A pdb=" N VAL B 92 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 125 through 128 Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 186 removed outlier: 9.202A pdb=" N LEU B 247 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR B 174 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 249 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER B 176 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.567A pdb=" N VAL C 92 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 125 through 128 Processing sheet with id=AB4, first strand: chain 'C' and resid 183 through 186 Processing sheet with id=AB5, first strand: chain 'D' and resid 267 through 270 removed outlier: 8.674A pdb=" N VAL D 342 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE D 258 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL D 344 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET D 260 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR D 346 " --> pdb=" O MET D 260 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY D 297 " --> pdb=" O THR D 345 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP E 35 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 118 through 119 removed outlier: 6.570A pdb=" N VAL D 92 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 128 Processing sheet with id=AB8, first strand: chain 'D' and resid 183 through 186 Processing sheet with id=AB9, first strand: chain 'E' and resid 267 through 270 removed outlier: 7.489A pdb=" N LYS E 256 " --> pdb=" O ASP E 340 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N VAL E 342 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE E 258 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL E 344 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET E 260 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR E 346 " --> pdb=" O MET E 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY E 297 " --> pdb=" O THR E 345 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE E 298 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP F 35 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 118 through 119 removed outlier: 6.572A pdb=" N VAL E 92 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 125 through 128 Processing sheet with id=AC3, first strand: chain 'E' and resid 183 through 186 removed outlier: 9.173A pdb=" N LEU E 247 " --> pdb=" O LYS E 172 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYR E 174 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL E 249 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N SER E 176 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 267 through 270 removed outlier: 7.483A pdb=" N LYS F 256 " --> pdb=" O ASP F 340 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N VAL F 342 " --> pdb=" O LYS F 256 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE F 258 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N VAL F 344 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET F 260 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N THR F 346 " --> pdb=" O MET F 260 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY F 297 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 298 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP G 35 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 118 through 119 removed outlier: 6.575A pdb=" N VAL F 92 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 125 through 128 Processing sheet with id=AC7, first strand: chain 'F' and resid 183 through 186 Processing sheet with id=AC8, first strand: chain 'G' and resid 267 through 270 removed outlier: 7.490A pdb=" N LYS G 256 " --> pdb=" O ASP G 340 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL G 342 " --> pdb=" O LYS G 256 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE G 258 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL G 344 " --> pdb=" O PHE G 258 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET G 260 " --> pdb=" O VAL G 344 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR G 346 " --> pdb=" O MET G 260 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY G 297 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE G 298 " --> pdb=" O LEU G 320 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP H 35 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 118 through 119 removed outlier: 6.582A pdb=" N VAL G 92 " --> pdb=" O ALA G 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 125 through 128 Processing sheet with id=AD2, first strand: chain 'G' and resid 183 through 186 removed outlier: 9.195A pdb=" N LEU G 247 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR G 174 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL G 249 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N SER G 176 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 118 through 119 removed outlier: 6.569A pdb=" N VAL H 92 " --> pdb=" O ALA H 166 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 125 through 128 Processing sheet with id=AD5, first strand: chain 'H' and resid 183 through 186 794 hydrogen bonds defined for protein. 2130 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: 11.57 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 21584 1.03 - 1.23: 83 1.23 - 1.42: 8869 1.42 - 1.61: 12856 1.61 - 1.81: 208 Bond restraints: 43600 Sorted by residual: bond pdb=" C GLN D 337 " pdb=" N PRO D 338 " ideal model delta sigma weight residual 1.334 1.346 -0.012 8.40e-03 1.42e+04 2.19e+00 bond pdb=" CB TYR C 110 " pdb=" CG TYR C 110 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.20e-02 2.07e+03 1.46e+00 bond pdb=" CB TYR B 110 " pdb=" CG TYR B 110 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.20e-02 2.07e+03 1.22e+00 bond pdb=" CA GLU G 262 " pdb=" C GLU G 262 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.14e-02 7.69e+03 9.33e-01 bond pdb=" CA GLU A 262 " pdb=" C GLU A 262 " ideal model delta sigma weight residual 1.530 1.519 0.011 1.14e-02 7.69e+03 9.16e-01 ... (remaining 43595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 75570 1.32 - 2.64: 3024 2.64 - 3.95: 212 3.95 - 5.27: 43 5.27 - 6.59: 7 Bond angle restraints: 78856 Sorted by residual: angle pdb=" N PRO D 338 " pdb=" CA PRO D 338 " pdb=" C PRO D 338 " ideal model delta sigma weight residual 114.68 118.79 -4.11 1.04e+00 9.25e-01 1.56e+01 angle pdb=" CA LEU F 255 " pdb=" C LEU F 255 " pdb=" N LYS F 256 " ideal model delta sigma weight residual 114.59 118.83 -4.24 1.48e+00 4.57e-01 8.21e+00 angle pdb=" CA VAL H 136 " pdb=" C VAL H 136 " pdb=" N VAL H 137 " ideal model delta sigma weight residual 116.60 120.61 -4.01 1.45e+00 4.76e-01 7.65e+00 angle pdb=" CA VAL C 136 " pdb=" C VAL C 136 " pdb=" N VAL C 137 " ideal model delta sigma weight residual 116.60 120.58 -3.98 1.45e+00 4.76e-01 7.53e+00 angle pdb=" CA VAL A 136 " pdb=" C VAL A 136 " pdb=" N VAL A 137 " ideal model delta sigma weight residual 116.60 120.56 -3.96 1.45e+00 4.76e-01 7.47e+00 ... (remaining 78851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 18199 16.88 - 33.76: 1363 33.76 - 50.64: 715 50.64 - 67.52: 226 67.52 - 84.40: 33 Dihedral angle restraints: 20536 sinusoidal: 11520 harmonic: 9016 Sorted by residual: dihedral pdb=" CA ARG D 335 " pdb=" C ARG D 335 " pdb=" N LEU D 336 " pdb=" CA LEU D 336 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA GLN D 337 " pdb=" C GLN D 337 " pdb=" N PRO D 338 " pdb=" CA PRO D 338 " ideal model delta harmonic sigma weight residual -180.00 -157.09 -22.91 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ALA F 186 " pdb=" C ALA F 186 " pdb=" N ILE F 187 " pdb=" CA ILE F 187 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 20533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2108 0.035 - 0.071: 909 0.071 - 0.106: 270 0.106 - 0.141: 139 0.141 - 0.177: 14 Chirality restraints: 3440 Sorted by residual: chirality pdb=" CA PRO D 338 " pdb=" N PRO D 338 " pdb=" C PRO D 338 " pdb=" CB PRO D 338 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA ILE E 187 " pdb=" N ILE E 187 " pdb=" C ILE E 187 " pdb=" CB ILE E 187 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA ILE B 187 " pdb=" N ILE B 187 " pdb=" C ILE B 187 " pdb=" CB ILE B 187 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 3437 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 337 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO D 338 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 338 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 338 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 24 " 0.028 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO C 25 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 25 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 25 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 128 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO E 129 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " -0.017 5.00e-02 4.00e+02 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 3783 2.22 - 2.82: 89792 2.82 - 3.41: 106251 3.41 - 4.01: 154319 4.01 - 4.60: 237191 Nonbonded interactions: 591336 Sorted by model distance: nonbonded pdb=" OE2 GLU B 221 " pdb="HH21 ARG B 223 " model vdw 1.627 2.450 nonbonded pdb=" O ASN H 236 " pdb="HH12 ARG H 239 " model vdw 1.627 2.450 nonbonded pdb=" OE2 GLU F 222 " pdb="HH21 ARG F 239 " model vdw 1.631 2.450 nonbonded pdb=" OE2 GLU D 222 " pdb="HH21 ARG D 239 " model vdw 1.637 2.450 nonbonded pdb=" OE2 GLU H 222 " pdb="HH21 ARG H 239 " model vdw 1.640 2.450 ... (remaining 591331 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' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.450 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: 0.250 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 40.910 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.004 0.044 22016 Z= 0.183 Angle : 0.631 6.589 29960 Z= 0.351 Chirality : 0.047 0.177 3440 Planarity : 0.005 0.053 3928 Dihedral : 15.103 84.404 8224 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.88 % Allowed : 12.84 % Favored : 86.28 % 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: -0.19 (0.15), residues: 2768 helix: 0.13 (0.19), residues: 792 sheet: 0.96 (0.22), residues: 520 loop : -0.64 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 223 TYR 0.014 0.003 TYR B 110 PHE 0.009 0.002 PHE B 168 TRP 0.007 0.002 TRP C 210 HIS 0.007 0.002 HIS E 135 Details of bonding type rmsd covalent geometry : bond 0.00423 (22016) covalent geometry : angle 0.63100 (29960) hydrogen bonds : bond 0.22326 ( 794) hydrogen bonds : angle 6.74381 ( 2130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 351 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8709 (tttt) cc_final: 0.8433 (tttm) REVERT: C 260 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8749 (mmm) REVERT: E 286 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8504 (mt-10) REVERT: E 346 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8452 (m) REVERT: F 290 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8246 (mmp) outliers start: 21 outliers final: 12 residues processed: 366 average time/residue: 1.4388 time to fit residues: 598.8045 Evaluate side-chains 360 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 345 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 146 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN F 353 ASN G 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.144812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120461 restraints weight = 64515.690| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.34 r_work: 0.2981 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22016 Z= 0.140 Angle : 0.564 6.781 29960 Z= 0.303 Chirality : 0.046 0.157 3440 Planarity : 0.005 0.044 3928 Dihedral : 5.445 56.130 3071 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.22 % Allowed : 11.33 % Favored : 86.45 % 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: -0.04 (0.16), residues: 2768 helix: 0.32 (0.19), residues: 800 sheet: 0.96 (0.21), residues: 520 loop : -0.54 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 223 TYR 0.010 0.002 TYR C 110 PHE 0.009 0.002 PHE A 258 TRP 0.008 0.001 TRP G 352 HIS 0.005 0.002 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00326 (22016) covalent geometry : angle 0.56358 (29960) hydrogen bonds : bond 0.05183 ( 794) hydrogen bonds : angle 5.20519 ( 2130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 401 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: A 265 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8341 (tttm) REVERT: B 260 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8598 (mmm) REVERT: B 280 GLU cc_start: 0.8984 (tt0) cc_final: 0.8706 (tt0) REVERT: C 109 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8122 (pp30) REVERT: C 260 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8365 (mtp) REVERT: C 290 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8408 (mmt) REVERT: D 230 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: D 260 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8215 (mmm) REVERT: E 109 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7890 (pp30) REVERT: E 260 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8550 (mmm) REVERT: E 265 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8237 (tttm) REVERT: E 280 GLU cc_start: 0.8925 (tt0) cc_final: 0.8687 (tt0) REVERT: F 109 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8154 (pp30) REVERT: F 260 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8236 (mmm) REVERT: G 109 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: G 286 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8582 (mt-10) REVERT: H 230 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7902 (tpp) REVERT: H 260 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8226 (mmm) REVERT: H 290 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8397 (mmt) outliers start: 53 outliers final: 18 residues processed: 362 average time/residue: 1.4208 time to fit residues: 587.4842 Evaluate side-chains 375 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 341 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 369 MET Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 290 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 178 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN G 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.143476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119402 restraints weight = 63683.226| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.31 r_work: 0.2941 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 22016 Z= 0.230 Angle : 0.652 7.790 29960 Z= 0.355 Chirality : 0.050 0.170 3440 Planarity : 0.006 0.061 3928 Dihedral : 5.158 37.111 3051 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.97 % Allowed : 12.16 % Favored : 85.86 % 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: -0.39 (0.15), residues: 2768 helix: -0.04 (0.18), residues: 800 sheet: 0.91 (0.20), residues: 520 loop : -0.79 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 111 TYR 0.014 0.003 TYR E 128 PHE 0.009 0.003 PHE F 258 TRP 0.006 0.002 TRP A 210 HIS 0.006 0.003 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00563 (22016) covalent geometry : angle 0.65210 (29960) hydrogen bonds : bond 0.06268 ( 794) hydrogen bonds : angle 5.13140 ( 2130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 393 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 346 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7405 (mpm) REVERT: A 109 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8187 (pp30) REVERT: A 265 LYS cc_start: 0.8580 (tttt) cc_final: 0.8300 (tttm) REVERT: B 37 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7935 (mt) REVERT: C 109 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8082 (pp30) REVERT: C 230 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: C 260 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8669 (mmm) REVERT: D 74 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7577 (mpm) REVERT: D 230 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8021 (mtp) REVERT: D 369 MET cc_start: 0.6607 (mtm) cc_final: 0.6388 (mmm) REVERT: E 109 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8158 (pp30) REVERT: E 265 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8243 (tttm) REVERT: F 109 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8213 (pp30) REVERT: G 109 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8110 (pp30) REVERT: G 286 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8601 (mt-10) REVERT: H 109 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8207 (pp30) REVERT: H 230 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8035 (mtp) outliers start: 47 outliers final: 19 residues processed: 359 average time/residue: 1.3829 time to fit residues: 567.1335 Evaluate side-chains 367 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 335 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 369 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 290 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 125 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN C 353 ASN D 353 ASN E 353 ASN G 353 ASN H 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120043 restraints weight = 66138.535| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.38 r_work: 0.3007 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22016 Z= 0.096 Angle : 0.493 5.206 29960 Z= 0.262 Chirality : 0.045 0.147 3440 Planarity : 0.004 0.038 3928 Dihedral : 4.630 36.383 3051 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.64 % Allowed : 12.46 % Favored : 85.91 % 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: 0.01 (0.16), residues: 2768 helix: 0.53 (0.19), residues: 800 sheet: 0.89 (0.21), residues: 512 loop : -0.57 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 223 TYR 0.006 0.001 TYR E 128 PHE 0.006 0.001 PHE B 258 TRP 0.007 0.001 TRP E 352 HIS 0.003 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00221 (22016) covalent geometry : angle 0.49281 (29960) hydrogen bonds : bond 0.03898 ( 794) hydrogen bonds : angle 4.73664 ( 2130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 390 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 351 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7095 (mpm) REVERT: A 109 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8169 (pp30) REVERT: A 265 LYS cc_start: 0.8470 (tttt) cc_final: 0.8206 (tttt) REVERT: B 280 GLU cc_start: 0.8911 (tt0) cc_final: 0.8662 (tt0) REVERT: C 109 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8168 (pp30) REVERT: C 260 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8555 (mtp) REVERT: D 74 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7427 (mpm) REVERT: D 230 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7980 (mtp) REVERT: D 260 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: D 369 MET cc_start: 0.6512 (mtm) cc_final: 0.6212 (mmm) REVERT: E 109 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8185 (pp30) REVERT: E 265 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8167 (tttm) REVERT: E 280 GLU cc_start: 0.8858 (tt0) cc_final: 0.8650 (tt0) REVERT: F 260 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8287 (mmm) REVERT: G 109 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8151 (pp30) REVERT: H 74 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7251 (mpm) REVERT: H 223 ARG cc_start: 0.8446 (mmt90) cc_final: 0.8220 (mmt90) REVERT: H 260 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8246 (mmm) outliers start: 39 outliers final: 14 residues processed: 357 average time/residue: 1.3885 time to fit residues: 566.6370 Evaluate side-chains 363 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 337 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 369 MET Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 115 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 224 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN G 353 ASN H 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107028 restraints weight = 66748.884| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.43 r_work: 0.2963 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22016 Z= 0.129 Angle : 0.522 5.659 29960 Z= 0.280 Chirality : 0.046 0.158 3440 Planarity : 0.005 0.046 3928 Dihedral : 4.642 35.349 3051 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.89 % Allowed : 12.21 % Favored : 85.91 % 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: 0.02 (0.16), residues: 2768 helix: 0.55 (0.19), residues: 800 sheet: 0.90 (0.20), residues: 512 loop : -0.58 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 223 TYR 0.008 0.002 TYR E 128 PHE 0.006 0.001 PHE E 258 TRP 0.007 0.001 TRP E 352 HIS 0.004 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00308 (22016) covalent geometry : angle 0.52175 (29960) hydrogen bonds : bond 0.04406 ( 794) hydrogen bonds : angle 4.72135 ( 2130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 386 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 341 time to evaluate : 1.244 Fit side-chains REVERT: A 74 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7191 (mpm) REVERT: A 109 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8156 (pp30) REVERT: A 220 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7571 (ttm170) REVERT: A 265 LYS cc_start: 0.8514 (tttt) cc_final: 0.8249 (tttt) REVERT: A 346 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8518 (m) REVERT: B 280 GLU cc_start: 0.8927 (tt0) cc_final: 0.8714 (tt0) REVERT: B 286 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8594 (mt-10) REVERT: C 109 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8101 (pp30) REVERT: C 223 ARG cc_start: 0.8478 (mmt90) cc_final: 0.8255 (mmt90) REVERT: D 74 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7491 (mpm) REVERT: D 369 MET cc_start: 0.6538 (mtm) cc_final: 0.6228 (mmm) REVERT: E 109 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8168 (pp30) REVERT: E 265 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8234 (tttm) REVERT: G 109 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8105 (pp30) REVERT: H 74 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7290 (mpm) REVERT: H 223 ARG cc_start: 0.8501 (mmt90) cc_final: 0.8283 (mmt90) REVERT: H 265 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8101 (mttm) outliers start: 45 outliers final: 20 residues processed: 355 average time/residue: 1.4129 time to fit residues: 573.0336 Evaluate side-chains 366 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 337 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 369 MET Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 265 LYS Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 40 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN F 353 ASN G 353 ASN H 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.122461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.098625 restraints weight = 62377.446| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.28 r_work: 0.2823 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22016 Z= 0.161 Angle : 0.561 6.007 29960 Z= 0.303 Chirality : 0.047 0.161 3440 Planarity : 0.005 0.052 3928 Dihedral : 4.729 25.909 3048 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.22 % Allowed : 12.29 % Favored : 85.49 % 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: -0.16 (0.15), residues: 2768 helix: 0.32 (0.19), residues: 800 sheet: 0.90 (0.20), residues: 520 loop : -0.70 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 223 TYR 0.010 0.002 TYR E 128 PHE 0.008 0.002 PHE B 258 TRP 0.005 0.001 TRP A 352 HIS 0.004 0.002 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00388 (22016) covalent geometry : angle 0.56104 (29960) hydrogen bonds : bond 0.04889 ( 794) hydrogen bonds : angle 4.80017 ( 2130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 387 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 334 time to evaluate : 1.028 Fit side-chains REVERT: A 74 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7283 (mpm) REVERT: A 109 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8106 (pp30) REVERT: A 265 LYS cc_start: 0.8570 (tttt) cc_final: 0.8339 (tttm) REVERT: A 346 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8645 (m) REVERT: B 37 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7931 (mt) REVERT: B 109 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8029 (pp30) REVERT: B 280 GLU cc_start: 0.8975 (tt0) cc_final: 0.8696 (tt0) REVERT: B 346 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8650 (m) REVERT: C 109 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8160 (pp30) REVERT: C 260 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8460 (mtp) REVERT: D 74 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7665 (mpm) REVERT: D 223 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8332 (mmt90) REVERT: D 260 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: D 369 MET cc_start: 0.6792 (mtm) cc_final: 0.6546 (mmm) REVERT: E 109 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8182 (pp30) REVERT: E 223 ARG cc_start: 0.8495 (mmt90) cc_final: 0.8207 (tpp80) REVERT: E 265 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8351 (tttm) REVERT: E 346 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8618 (m) REVERT: F 260 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8302 (mmm) REVERT: G 109 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8154 (pp30) REVERT: H 22 THR cc_start: 0.5784 (OUTLIER) cc_final: 0.5544 (t) REVERT: H 74 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7521 (mpm) REVERT: H 230 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8132 (mtp) REVERT: H 260 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8273 (mmm) outliers start: 53 outliers final: 25 residues processed: 353 average time/residue: 1.4535 time to fit residues: 583.3038 Evaluate side-chains 378 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 335 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 369 MET Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 204 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 266 optimal weight: 0.0030 chunk 90 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN G 353 ASN H 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.136269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110524 restraints weight = 64698.378| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.36 r_work: 0.2910 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22016 Z= 0.153 Angle : 0.548 5.799 29960 Z= 0.295 Chirality : 0.047 0.159 3440 Planarity : 0.005 0.051 3928 Dihedral : 4.695 25.975 3048 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.27 % Allowed : 12.42 % Favored : 85.32 % 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: -0.18 (0.15), residues: 2768 helix: 0.33 (0.19), residues: 800 sheet: 0.93 (0.20), residues: 512 loop : -0.73 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 223 TYR 0.010 0.002 TYR A 128 PHE 0.007 0.002 PHE B 258 TRP 0.006 0.001 TRP E 352 HIS 0.004 0.002 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00369 (22016) covalent geometry : angle 0.54847 (29960) hydrogen bonds : bond 0.04691 ( 794) hydrogen bonds : angle 4.75581 ( 2130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7164 (mpm) REVERT: A 109 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8157 (pp30) REVERT: A 265 LYS cc_start: 0.8523 (tttt) cc_final: 0.8271 (tttm) REVERT: A 286 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 346 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8528 (m) REVERT: B 37 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7930 (mt) REVERT: B 280 GLU cc_start: 0.8917 (tt0) cc_final: 0.8638 (tt0) REVERT: C 109 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8152 (pp30) REVERT: C 223 ARG cc_start: 0.8443 (mmt90) cc_final: 0.8183 (mmt90) REVERT: D 74 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7550 (mpm) REVERT: D 223 ARG cc_start: 0.8472 (mmt90) cc_final: 0.8267 (mmt90) REVERT: D 230 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8058 (mtp) REVERT: D 260 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8265 (mmm) REVERT: D 369 MET cc_start: 0.6576 (mtm) cc_final: 0.6355 (mmm) REVERT: E 109 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8185 (pp30) REVERT: E 223 ARG cc_start: 0.8436 (mmt90) cc_final: 0.8129 (tpp80) REVERT: E 265 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8249 (tttm) REVERT: E 346 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8511 (m) REVERT: F 260 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: G 109 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8113 (pp30) REVERT: H 22 THR cc_start: 0.5736 (OUTLIER) cc_final: 0.5526 (t) REVERT: H 74 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7385 (mpm) REVERT: H 223 ARG cc_start: 0.8405 (mmt90) cc_final: 0.8141 (mmt90) REVERT: H 260 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8221 (mmm) outliers start: 54 outliers final: 27 residues processed: 358 average time/residue: 1.4300 time to fit residues: 582.4508 Evaluate side-chains 379 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 369 MET Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 21 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 231 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN G 353 ASN H 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113075 restraints weight = 64610.806| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.35 r_work: 0.2895 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22016 Z= 0.144 Angle : 0.539 5.910 29960 Z= 0.290 Chirality : 0.046 0.158 3440 Planarity : 0.005 0.049 3928 Dihedral : 4.657 25.729 3048 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.06 % Allowed : 13.13 % Favored : 84.82 % 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: -0.16 (0.15), residues: 2768 helix: 0.36 (0.19), residues: 800 sheet: 0.94 (0.20), residues: 512 loop : -0.73 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 223 TYR 0.009 0.002 TYR A 128 PHE 0.007 0.002 PHE G 258 TRP 0.006 0.001 TRP A 352 HIS 0.004 0.002 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00347 (22016) covalent geometry : angle 0.53936 (29960) hydrogen bonds : bond 0.04571 ( 794) hydrogen bonds : angle 4.72205 ( 2130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 388 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 339 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7147 (mpm) REVERT: A 109 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8192 (pp30) REVERT: A 220 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7652 (ttm170) REVERT: A 265 LYS cc_start: 0.8493 (tttt) cc_final: 0.8234 (tttm) REVERT: A 286 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8586 (mt-10) REVERT: A 346 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8507 (m) REVERT: B 223 ARG cc_start: 0.8423 (mmt90) cc_final: 0.8035 (tpp80) REVERT: B 280 GLU cc_start: 0.8912 (tt0) cc_final: 0.8629 (tt0) REVERT: B 346 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8525 (m) REVERT: C 109 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8163 (pp30) REVERT: C 223 ARG cc_start: 0.8464 (mmt90) cc_final: 0.8211 (mmt90) REVERT: D 74 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7558 (mpm) REVERT: D 260 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8299 (mmm) REVERT: D 369 MET cc_start: 0.6738 (mtm) cc_final: 0.6510 (mmm) REVERT: E 109 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8175 (pp30) REVERT: E 223 ARG cc_start: 0.8462 (mmt90) cc_final: 0.8143 (tpp80) REVERT: E 265 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8242 (tttm) REVERT: E 346 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8509 (m) REVERT: F 260 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8220 (mmm) REVERT: G 109 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8116 (pp30) REVERT: G 286 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8583 (mt-10) REVERT: H 74 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7395 (mpm) REVERT: H 223 ARG cc_start: 0.8435 (mmt90) cc_final: 0.8184 (mmt90) REVERT: H 260 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8265 (mmm) outliers start: 49 outliers final: 29 residues processed: 354 average time/residue: 1.3288 time to fit residues: 536.3854 Evaluate side-chains 374 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 332 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 357 ASN Chi-restraints excluded: chain G residue 369 MET Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 48 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN F 232 ASN G 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.107306 restraints weight = 65630.579| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.38 r_work: 0.2877 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22016 Z= 0.179 Angle : 0.582 6.401 29960 Z= 0.314 Chirality : 0.048 0.163 3440 Planarity : 0.005 0.054 3928 Dihedral : 4.793 25.983 3048 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.14 % Allowed : 13.21 % Favored : 84.65 % 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: -0.28 (0.15), residues: 2768 helix: 0.22 (0.19), residues: 800 sheet: 0.93 (0.20), residues: 520 loop : -0.81 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 223 TYR 0.014 0.003 TYR C 110 PHE 0.008 0.002 PHE G 258 TRP 0.007 0.002 TRP B 352 HIS 0.005 0.002 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00437 (22016) covalent geometry : angle 0.58166 (29960) hydrogen bonds : bond 0.05100 ( 794) hydrogen bonds : angle 4.81663 ( 2130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 383 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 332 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7220 (mpm) REVERT: A 109 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8131 (pp30) REVERT: A 220 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7670 (ttm170) REVERT: A 265 LYS cc_start: 0.8513 (tttt) cc_final: 0.8236 (tttm) REVERT: A 286 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8628 (mt-10) REVERT: B 37 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7926 (mt) REVERT: B 223 ARG cc_start: 0.8436 (mmt90) cc_final: 0.8074 (tpp80) REVERT: B 346 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8588 (m) REVERT: C 109 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8167 (pp30) REVERT: C 223 ARG cc_start: 0.8474 (mmt90) cc_final: 0.8220 (mmt90) REVERT: C 230 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: D 74 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7566 (mpm) REVERT: D 223 ARG cc_start: 0.8435 (mmt90) cc_final: 0.8171 (mmt90) REVERT: D 260 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8296 (mmm) REVERT: D 369 MET cc_start: 0.6754 (mtm) cc_final: 0.6505 (mmm) REVERT: E 109 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8172 (pp30) REVERT: E 223 ARG cc_start: 0.8472 (mmt90) cc_final: 0.8134 (tpp80) REVERT: E 265 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8250 (tttm) REVERT: E 346 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8564 (m) REVERT: F 260 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8187 (mmm) REVERT: G 109 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8124 (pp30) REVERT: H 74 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7440 (mpm) REVERT: H 223 ARG cc_start: 0.8446 (mmt90) cc_final: 0.8191 (mmt90) REVERT: H 260 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8253 (mmm) outliers start: 51 outliers final: 24 residues processed: 349 average time/residue: 1.2523 time to fit residues: 499.8225 Evaluate side-chains 369 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 331 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 186 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN G 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112380 restraints weight = 65148.243| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.29 r_work: 0.2912 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22016 Z= 0.147 Angle : 0.544 6.028 29960 Z= 0.292 Chirality : 0.046 0.158 3440 Planarity : 0.005 0.048 3928 Dihedral : 4.691 25.827 3048 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.55 % Allowed : 13.72 % Favored : 84.73 % 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: -0.21 (0.15), residues: 2768 helix: 0.32 (0.19), residues: 800 sheet: 0.94 (0.20), residues: 512 loop : -0.78 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 223 TYR 0.019 0.002 TYR D 110 PHE 0.006 0.002 PHE B 258 TRP 0.007 0.001 TRP B 352 HIS 0.004 0.002 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00354 (22016) covalent geometry : angle 0.54411 (29960) hydrogen bonds : bond 0.04585 ( 794) hydrogen bonds : angle 4.73733 ( 2130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Residue THR 22 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 333 time to evaluate : 1.066 Fit side-chains REVERT: A 74 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7165 (mpm) REVERT: A 109 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8132 (pp30) REVERT: A 220 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7703 (ttm170) REVERT: A 265 LYS cc_start: 0.8491 (tttt) cc_final: 0.8238 (tttm) REVERT: A 286 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8601 (mt-10) REVERT: B 37 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7952 (mt) REVERT: B 223 ARG cc_start: 0.8413 (mmt90) cc_final: 0.8070 (tpp80) REVERT: B 280 GLU cc_start: 0.8923 (tt0) cc_final: 0.8658 (tt0) REVERT: B 346 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8545 (m) REVERT: C 109 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8096 (pp30) REVERT: C 223 ARG cc_start: 0.8466 (mmt90) cc_final: 0.8233 (mmt90) REVERT: D 74 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7557 (mpm) REVERT: D 223 ARG cc_start: 0.8436 (mmt90) cc_final: 0.8196 (mmt90) REVERT: D 260 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8258 (mmm) REVERT: D 369 MET cc_start: 0.6620 (mtm) cc_final: 0.6361 (mmm) REVERT: E 109 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8172 (pp30) REVERT: E 223 ARG cc_start: 0.8458 (mmt90) cc_final: 0.8149 (tpp80) REVERT: E 265 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8246 (tttm) REVERT: E 346 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8523 (m) REVERT: F 260 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8239 (mmm) REVERT: G 109 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8124 (pp30) REVERT: H 74 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7411 (mpm) REVERT: H 223 ARG cc_start: 0.8441 (mmt90) cc_final: 0.8210 (mmt90) REVERT: H 260 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8228 (mmm) outliers start: 37 outliers final: 23 residues processed: 347 average time/residue: 1.0646 time to fit residues: 424.9056 Evaluate side-chains 362 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 326 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 369 MET Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 260 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 369 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 167 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 226 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 353 ASN E 353 ASN G 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.136773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.112717 restraints weight = 65334.822| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.29 r_work: 0.2917 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22016 Z= 0.138 Angle : 0.536 5.994 29960 Z= 0.287 Chirality : 0.046 0.156 3440 Planarity : 0.005 0.048 3928 Dihedral : 4.635 25.618 3048 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.72 % Allowed : 13.67 % Favored : 84.61 % 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: -0.17 (0.15), residues: 2768 helix: 0.37 (0.19), residues: 800 sheet: 0.94 (0.20), residues: 512 loop : -0.76 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 223 TYR 0.019 0.002 TYR C 110 PHE 0.007 0.002 PHE B 258 TRP 0.008 0.001 TRP G 352 HIS 0.004 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00332 (22016) covalent geometry : angle 0.53556 (29960) hydrogen bonds : bond 0.04456 ( 794) hydrogen bonds : angle 4.69553 ( 2130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13696.87 seconds wall clock time: 231 minutes 34.13 seconds (13894.13 seconds total)