Starting phenix.real_space_refine on Wed Apr 8 20:30:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r60_53598/04_2026/9r60_53598_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r60_53598/04_2026/9r60_53598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r60_53598/04_2026/9r60_53598_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r60_53598/04_2026/9r60_53598_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r60_53598/04_2026/9r60_53598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r60_53598/04_2026/9r60_53598.map" } resolution = 3.0 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= 0.049 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 115 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: 7.49, per 1000 atoms: 0.17 Number of scatterers: 43200 At special positions: 0 Unit cell: (122.85, 122.85, 139.23, 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: 3.55 Conformation dependent library (CDL) restraints added in 1.1 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: 119 helices and 32 sheets defined 33.0% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 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 removed outlier: 3.606A pdb=" N ASN A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 140 through 153 removed outlier: 3.550A 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: 4.036A 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: 3.565A pdb=" N ALA A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 removed outlier: 4.148A 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 140 through 153 removed outlier: 3.546A 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 233 Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 251 through 254 removed outlier: 4.078A 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: 3.508A 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: 3.652A pdb=" N ALA B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 removed outlier: 3.578A pdb=" N LEU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 369 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.536A pdb=" N LYS C 48 " --> pdb=" O ASP C 45 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.521A pdb=" N ALA C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) 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: 4.166A 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: 3.534A pdb=" N ALA C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 removed outlier: 4.046A pdb=" N GLN C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 369 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 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 140 through 153 removed outlier: 3.562A pdb=" N ALA D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) 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: 3.961A 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: 3.816A pdb=" N GLY D 309 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.531A pdb=" N ALA D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 357 removed outlier: 3.550A pdb=" N LEU D 355 " --> pdb=" O ARG D 351 " (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 113 through 117 removed outlier: 4.071A pdb=" N GLY E 117 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 153 removed outlier: 3.607A pdb=" N ALA E 153 " --> pdb=" O THR E 149 " (cutoff:3.500A) 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: 3.930A 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: 3.589A pdb=" N ALA E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 357 removed outlier: 3.620A pdb=" N LEU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 369 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 removed outlier: 3.523A pdb=" N ALA F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 201 Processing helix chain 'F' and resid 225 through 233 Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 251 through 254 removed outlier: 3.982A 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 307 through 312 removed outlier: 4.377A pdb=" N ASN F 311 " --> pdb=" O GLU F 307 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 347 through 357 Processing helix chain 'F' and resid 359 through 369 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.529A 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 112 through 116 Processing helix chain 'G' and resid 140 through 153 removed outlier: 3.528A 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: 4.203A 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 Processing helix chain 'G' and resid 347 through 357 removed outlier: 3.546A pdb=" N LEU G 355 " --> pdb=" O ARG G 351 " (cutoff:3.500A) 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 removed outlier: 3.574A pdb=" N ALA H 153 " --> pdb=" O THR H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 201 Processing helix chain 'H' and resid 225 through 233 Processing helix chain 'H' and resid 234 through 238 Processing helix chain 'H' and resid 251 through 254 removed outlier: 4.071A 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: 3.599A pdb=" N ALA H 331 " --> pdb=" O SER H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 358 removed outlier: 3.879A 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: 6.900A pdb=" N ASP A 35 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 298 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY C 297 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP C 340 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.476A pdb=" N GLY A 297 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 298 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 4.444A 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: 6.690A 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 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.925A pdb=" N ASP B 35 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE H 298 " --> pdb=" O LEU H 320 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR H 345 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N SER H 296 " --> pdb=" O TYR H 343 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N TYR H 343 " --> pdb=" O SER H 296 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ILE H 298 " --> pdb=" O VAL H 341 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N VAL H 341 " --> pdb=" O ILE H 298 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS H 256 " --> pdb=" O ASP H 340 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N VAL H 342 " --> pdb=" O LYS H 256 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE H 258 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL H 344 " --> pdb=" O PHE H 258 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET H 260 " --> pdb=" O VAL H 344 " (cutoff:3.500A) removed outlier: 8.460A 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: 4.038A pdb=" N ASP B 340 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY B 297 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 298 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 4.349A 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: 6.404A 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 Processing sheet with id=AB2, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.780A 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: 3.569A pdb=" N THR D 345 " --> pdb=" O GLY D 297 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY D 297 " --> pdb=" O THR D 345 " (cutoff:3.500A) removed outlier: 4.545A 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: 6.642A 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: 7.552A pdb=" N LYS E 256 " --> pdb=" O ASP E 340 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N VAL E 342 " --> pdb=" O LYS E 256 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE E 258 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL E 344 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET E 260 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR E 346 " --> pdb=" O MET E 260 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY E 297 " --> pdb=" O THR E 345 " (cutoff:3.500A) removed outlier: 4.345A 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: 6.724A 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: 9.210A pdb=" N LEU E 247 " --> pdb=" O LYS E 172 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR E 174 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL E 249 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 7.132A 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: 4.110A pdb=" N ASP F 340 " --> pdb=" O LYS F 256 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLY F 297 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE F 298 " --> pdb=" O LEU F 320 " (cutoff:3.500A) removed outlier: 4.354A 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: 6.788A 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 50 through 54 removed outlier: 3.641A pdb=" N ILE G 298 " --> pdb=" O LEU G 320 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY G 297 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP G 340 " --> pdb=" O LYS G 256 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 118 through 119 removed outlier: 6.565A 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: 9.282A pdb=" N LEU G 247 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR G 174 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL G 249 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 7.382A 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: 6.361A 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 removed outlier: 3.550A pdb=" N VAL H 249 " --> pdb=" O SER H 176 " (cutoff:3.500A) 821 hydrogen bonds defined for protein. 2196 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: 11.65 Time building geometry restraints manager: 5.08 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: 351 1.23 - 1.43: 8602 1.43 - 1.62: 12854 1.62 - 1.82: 209 Bond restraints: 43600 Sorted by residual: bond pdb=" CB PRO D 65 " pdb=" CG PRO D 65 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.11e+00 bond pdb=" N PRO D 65 " pdb=" CD PRO D 65 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.60e+00 bond pdb=" CG PRO D 65 " pdb=" CD PRO D 65 " ideal model delta sigma weight residual 1.503 1.422 0.081 3.40e-02 8.65e+02 5.62e+00 bond pdb=" N PRO D 65 " pdb=" CA PRO D 65 " ideal model delta sigma weight residual 1.465 1.440 0.024 1.12e-02 7.97e+03 4.63e+00 bond pdb=" CB PRO G 65 " pdb=" CG PRO G 65 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.70e+00 ... (remaining 43595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 78679 3.08 - 6.17: 172 6.17 - 9.25: 1 9.25 - 12.33: 3 12.33 - 15.41: 1 Bond angle restraints: 78856 Sorted by residual: angle pdb=" CA PRO D 65 " pdb=" N PRO D 65 " pdb=" CD PRO D 65 " ideal model delta sigma weight residual 112.00 96.59 15.41 1.40e+00 5.10e-01 1.21e+02 angle pdb=" N PRO D 65 " pdb=" CD PRO D 65 " pdb=" CG PRO D 65 " ideal model delta sigma weight residual 103.20 95.16 8.04 1.50e+00 4.44e-01 2.87e+01 angle pdb=" CA PRO G 65 " pdb=" N PRO G 65 " pdb=" CD PRO G 65 " ideal model delta sigma weight residual 112.00 105.99 6.01 1.40e+00 5.10e-01 1.84e+01 angle pdb=" CB ARG F 220 " pdb=" CG ARG F 220 " pdb=" CD ARG F 220 " ideal model delta sigma weight residual 111.30 120.98 -9.68 2.30e+00 1.89e-01 1.77e+01 angle pdb=" N PRO D 65 " pdb=" CD PRO D 65 " pdb=" HD2 PRO D 65 " ideal model delta sigma weight residual 109.00 121.27 -12.27 3.00e+00 1.11e-01 1.67e+01 ... (remaining 78851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18342 17.98 - 35.96: 1362 35.96 - 53.95: 626 53.95 - 71.93: 175 71.93 - 89.91: 31 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 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+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 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CG ARG G 223 " pdb=" CD ARG G 223 " pdb=" NE ARG G 223 " pdb=" CZ ARG G 223 " ideal model delta sinusoidal sigma weight residual -90.00 -40.07 -49.93 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 20533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2708 0.049 - 0.097: 504 0.097 - 0.146: 225 0.146 - 0.195: 2 0.195 - 0.243: 1 Chirality restraints: 3440 Sorted by residual: chirality pdb=" CA PRO D 65 " pdb=" N PRO D 65 " pdb=" C PRO D 65 " pdb=" CB PRO D 65 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.48e+00 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 2.55 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE C 187 " pdb=" N ILE C 187 " pdb=" C ILE C 187 " pdb=" CB ILE C 187 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 3437 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 64 " -0.097 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO D 65 " 0.231 5.00e-02 4.00e+02 pdb=" CA PRO D 65 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 65 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 64 " 0.054 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO G 65 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 65 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 65 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 71 " -0.242 9.50e-02 1.11e+02 8.11e-02 8.04e+00 pdb=" NE ARG H 71 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG H 71 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 71 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 71 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG H 71 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG H 71 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG H 71 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 71 " 0.000 2.00e-02 2.50e+03 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 893 2.13 - 2.75: 76605 2.75 - 3.36: 114254 3.36 - 3.98: 152699 3.98 - 4.60: 243932 Nonbonded interactions: 588383 Sorted by model distance: nonbonded pdb=" O ASN A 353 " pdb="HD21 ASN A 357 " model vdw 1.509 2.450 nonbonded pdb=" HG1 THR H 193 " pdb=" OD1 ASP H 196 " model vdw 1.525 2.450 nonbonded pdb=" O ASN E 236 " pdb="HH12 ARG E 239 " model vdw 1.553 2.450 nonbonded pdb=" O ASN B 236 " pdb="HH12 ARG B 239 " model vdw 1.592 2.450 nonbonded pdb=" O ASN H 236 " pdb="HH12 ARG H 239 " model vdw 1.615 2.450 ... (remaining 588378 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: 1.060 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: 0.230 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 39.970 Find NCS groups from input model: 0.560 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: 0.000 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 0.133 22016 Z= 0.171 Angle : 0.595 15.415 29960 Z= 0.334 Chirality : 0.046 0.243 3440 Planarity : 0.006 0.134 3928 Dihedral : 15.199 89.912 8224 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.05 % Allowed : 13.63 % 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: 0.01 (0.16), residues: 2768 helix: 0.25 (0.19), residues: 800 sheet: 0.71 (0.23), residues: 504 loop : -0.29 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 71 TYR 0.025 0.002 TYR B 110 PHE 0.009 0.001 PHE F 168 TRP 0.009 0.001 TRP F 352 HIS 0.004 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00403 (22016) covalent geometry : angle 0.59494 (29960) hydrogen bonds : bond 0.22564 ( 821) hydrogen bonds : angle 7.68624 ( 2196) *********************** 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 284 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7329 (mm-30) REVERT: C 310 ARG cc_start: 0.5413 (OUTLIER) cc_final: 0.5159 (ptp-170) REVERT: D 234 ASP cc_start: 0.8683 (t0) cc_final: 0.8481 (t0) REVERT: E 32 MET cc_start: 0.8214 (mmm) cc_final: 0.7989 (tpt) REVERT: F 220 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7376 (ttp80) REVERT: G 260 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8384 (mtp) outliers start: 25 outliers final: 18 residues processed: 279 average time/residue: 1.5868 time to fit residues: 499.7441 Evaluate side-chains 272 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain H residue 79 GLU Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 176 SER Chi-restraints excluded: chain H residue 327 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN B 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.100258 restraints weight = 84203.513| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.88 r_work: 0.2942 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22016 Z= 0.146 Angle : 0.540 6.126 29960 Z= 0.291 Chirality : 0.046 0.149 3440 Planarity : 0.005 0.051 3928 Dihedral : 5.226 48.506 3082 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.96 % Allowed : 13.38 % Favored : 85.65 % 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: -0.10 (0.16), residues: 2768 helix: 0.22 (0.19), residues: 816 sheet: 0.75 (0.22), residues: 496 loop : -0.46 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 220 TYR 0.012 0.001 TYR E 110 PHE 0.008 0.001 PHE F 168 TRP 0.011 0.001 TRP F 352 HIS 0.005 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00342 (22016) covalent geometry : angle 0.54000 (29960) hydrogen bonds : bond 0.05548 ( 821) hydrogen bonds : angle 5.71493 ( 2196) *********************** 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 284 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: C 109 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7781 (pt0) REVERT: D 158 ASP cc_start: 0.8248 (t0) cc_final: 0.7985 (t0) REVERT: D 265 LYS cc_start: 0.8695 (ttmp) cc_final: 0.8425 (ttpp) REVERT: E 32 MET cc_start: 0.8351 (mmm) cc_final: 0.8125 (tpt) REVERT: F 206 ASP cc_start: 0.7996 (m-30) cc_final: 0.7569 (m-30) REVERT: F 264 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8743 (mttt) REVERT: F 286 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: G 260 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8393 (mtp) outliers start: 23 outliers final: 6 residues processed: 273 average time/residue: 1.4244 time to fit residues: 442.0498 Evaluate side-chains 257 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 247 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 126 MET Chi-restraints excluded: chain H residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 178 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 66 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: B 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.099090 restraints weight = 83853.436| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.93 r_work: 0.2902 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22016 Z= 0.192 Angle : 0.551 5.448 29960 Z= 0.297 Chirality : 0.047 0.158 3440 Planarity : 0.005 0.046 3928 Dihedral : 4.839 39.160 3057 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.17 % Allowed : 14.05 % Favored : 84.77 % 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: -0.31 (0.16), residues: 2768 helix: 0.10 (0.18), residues: 816 sheet: 0.62 (0.22), residues: 496 loop : -0.62 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 220 TYR 0.012 0.002 TYR E 339 PHE 0.010 0.001 PHE F 168 TRP 0.007 0.001 TRP F 352 HIS 0.004 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00467 (22016) covalent geometry : angle 0.55093 (29960) hydrogen bonds : bond 0.05314 ( 821) hydrogen bonds : angle 5.40245 ( 2196) *********************** 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 285 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 353 ASN cc_start: 0.8542 (t0) cc_final: 0.8336 (t0) REVERT: A 357 ASN cc_start: 0.8824 (m-40) cc_final: 0.8436 (m110) REVERT: C 109 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7811 (pt0) REVERT: C 121 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: C 260 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: D 158 ASP cc_start: 0.8104 (t0) cc_final: 0.7813 (t0) REVERT: D 221 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: E 32 MET cc_start: 0.8330 (mmm) cc_final: 0.8104 (tpt) REVERT: F 260 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8202 (mtt) REVERT: F 264 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8789 (mttt) REVERT: G 260 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8370 (mtp) outliers start: 28 outliers final: 8 residues processed: 275 average time/residue: 1.4345 time to fit residues: 449.4402 Evaluate side-chains 261 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 246 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 176 SER 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: 1.9990 chunk 116 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 78 optimal weight: 0.0060 chunk 18 optimal weight: 4.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.103591 restraints weight = 83129.353| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.91 r_work: 0.2965 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22016 Z= 0.088 Angle : 0.469 4.752 29960 Z= 0.247 Chirality : 0.044 0.145 3440 Planarity : 0.004 0.047 3928 Dihedral : 4.419 36.045 3057 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.59 % Allowed : 14.72 % Favored : 84.69 % 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 (0.16), residues: 2768 helix: 0.75 (0.20), residues: 800 sheet: 0.56 (0.22), residues: 496 loop : -0.35 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 223 TYR 0.009 0.001 TYR E 110 PHE 0.006 0.001 PHE G 258 TRP 0.008 0.001 TRP G 352 HIS 0.002 0.001 HIS E 100 Details of bonding type rmsd covalent geometry : bond 0.00201 (22016) covalent geometry : angle 0.46878 (29960) hydrogen bonds : bond 0.03642 ( 821) hydrogen bonds : angle 4.94390 ( 2196) *********************** 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 287 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 273 time to evaluate : 1.208 Fit side-chains REVERT: A 353 ASN cc_start: 0.8507 (t0) cc_final: 0.8279 (t0) REVERT: A 357 ASN cc_start: 0.8789 (m-40) cc_final: 0.8362 (m110) REVERT: B 115 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: C 109 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7762 (pt0) REVERT: D 109 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: D 158 ASP cc_start: 0.8033 (t0) cc_final: 0.7695 (t0) REVERT: D 296 SER cc_start: 0.9072 (p) cc_final: 0.8826 (p) REVERT: E 32 MET cc_start: 0.8296 (mmm) cc_final: 0.8074 (tpt) REVERT: E 110 TYR cc_start: 0.7561 (t80) cc_final: 0.7333 (t80) REVERT: F 206 ASP cc_start: 0.7976 (m-30) cc_final: 0.7620 (m-30) REVERT: F 264 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8698 (mttt) REVERT: F 286 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8190 (mt-10) outliers start: 14 outliers final: 3 residues processed: 280 average time/residue: 1.4160 time to fit residues: 452.8992 Evaluate side-chains 265 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 286 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 115 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 255 optimal weight: 0.0670 chunk 250 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.123809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102045 restraints weight = 83223.944| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.90 r_work: 0.2952 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1445 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= 0.130 Angle : 0.492 4.839 29960 Z= 0.261 Chirality : 0.045 0.150 3440 Planarity : 0.004 0.052 3928 Dihedral : 4.250 23.309 3048 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.01 % Allowed : 14.77 % Favored : 84.23 % 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: 0.11 (0.16), residues: 2768 helix: 0.62 (0.19), residues: 816 sheet: 0.46 (0.20), residues: 592 loop : -0.36 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 223 TYR 0.010 0.001 TYR E 339 PHE 0.008 0.001 PHE F 168 TRP 0.006 0.001 TRP D 352 HIS 0.003 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00312 (22016) covalent geometry : angle 0.49203 (29960) hydrogen bonds : bond 0.04077 ( 821) hydrogen bonds : angle 4.92192 ( 2196) *********************** 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 284 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 353 ASN cc_start: 0.8524 (t0) cc_final: 0.8315 (t0) REVERT: A 357 ASN cc_start: 0.8788 (m-40) cc_final: 0.8349 (m110) REVERT: B 115 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: C 109 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: D 109 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: D 158 ASP cc_start: 0.8042 (t0) cc_final: 0.7677 (t0) REVERT: D 296 SER cc_start: 0.9031 (p) cc_final: 0.8795 (p) REVERT: E 32 MET cc_start: 0.8302 (mmm) cc_final: 0.8080 (tpt) REVERT: E 220 ARG cc_start: 0.7334 (ttp80) cc_final: 0.7014 (tpt-90) REVERT: E 260 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8232 (mtp) REVERT: F 264 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8691 (mttt) REVERT: F 286 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: G 109 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7759 (pt0) outliers start: 24 outliers final: 7 residues processed: 273 average time/residue: 1.3869 time to fit residues: 433.6344 Evaluate side-chains 266 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain H residue 99 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 40 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100391 restraints weight = 84356.705| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.95 r_work: 0.2943 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.005 0.047 22016 Z= 0.201 Angle : 0.546 5.186 29960 Z= 0.293 Chirality : 0.047 0.156 3440 Planarity : 0.005 0.057 3928 Dihedral : 4.531 24.217 3048 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.17 % Allowed : 15.27 % Favored : 83.56 % 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 (0.16), residues: 2768 helix: 0.31 (0.19), residues: 816 sheet: 0.35 (0.20), residues: 600 loop : -0.56 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 223 TYR 0.014 0.002 TYR E 339 PHE 0.011 0.001 PHE F 168 TRP 0.008 0.001 TRP F 98 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00493 (22016) covalent geometry : angle 0.54593 (29960) hydrogen bonds : bond 0.04770 ( 821) hydrogen bonds : angle 5.06555 ( 2196) *********************** 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 291 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 353 ASN cc_start: 0.8584 (t0) cc_final: 0.8368 (t0) REVERT: A 357 ASN cc_start: 0.8813 (m-40) cc_final: 0.8373 (m110) REVERT: B 115 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: C 109 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7788 (pt0) REVERT: D 109 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: D 158 ASP cc_start: 0.8061 (t0) cc_final: 0.7699 (t0) REVERT: D 221 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: D 296 SER cc_start: 0.9060 (p) cc_final: 0.8850 (p) REVERT: E 32 MET cc_start: 0.8280 (mmm) cc_final: 0.8058 (tpt) REVERT: E 220 ARG cc_start: 0.7362 (ttp80) cc_final: 0.7073 (tpt-90) REVERT: E 260 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8867 (mmm) REVERT: E 286 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8589 (mt-10) REVERT: F 264 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8758 (mttt) REVERT: F 286 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: G 260 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8307 (mtp) REVERT: G 353 ASN cc_start: 0.8587 (t0) cc_final: 0.8381 (t0) outliers start: 28 outliers final: 10 residues processed: 276 average time/residue: 1.3925 time to fit residues: 438.8705 Evaluate side-chains 272 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 176 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 204 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 90 optimal weight: 0.0870 chunk 162 optimal weight: 4.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.099888 restraints weight = 83832.022| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.95 r_work: 0.2936 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22016 Z= 0.207 Angle : 0.554 5.274 29960 Z= 0.298 Chirality : 0.047 0.156 3440 Planarity : 0.005 0.116 3928 Dihedral : 4.647 24.796 3048 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.34 % Allowed : 15.60 % Favored : 83.05 % 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: -0.40 (0.16), residues: 2768 helix: 0.15 (0.19), residues: 816 sheet: 0.32 (0.20), residues: 600 loop : -0.72 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 58 TYR 0.015 0.002 TYR E 339 PHE 0.010 0.001 PHE F 168 TRP 0.008 0.001 TRP C 352 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00508 (22016) covalent geometry : angle 0.55406 (29960) hydrogen bonds : bond 0.04797 ( 821) hydrogen bonds : angle 5.09600 ( 2196) *********************** 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 292 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8475 (t0) cc_final: 0.8224 (t0) REVERT: A 222 GLU cc_start: 0.8238 (tt0) cc_final: 0.8014 (tt0) REVERT: A 353 ASN cc_start: 0.8581 (t0) cc_final: 0.8359 (t0) REVERT: A 357 ASN cc_start: 0.8768 (m110) cc_final: 0.8337 (m110) REVERT: C 109 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: C 260 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8407 (mtp) REVERT: D 109 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: D 158 ASP cc_start: 0.8091 (t0) cc_final: 0.7666 (t0) REVERT: D 221 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: D 296 SER cc_start: 0.9058 (p) cc_final: 0.8833 (m) REVERT: E 220 ARG cc_start: 0.7372 (ttp80) cc_final: 0.7076 (tpt-90) REVERT: F 260 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8229 (mtt) REVERT: F 264 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8762 (mttt) REVERT: G 143 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8268 (mt-10) REVERT: G 221 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: G 260 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8379 (mtp) REVERT: G 353 ASN cc_start: 0.8633 (t0) cc_final: 0.8410 (t0) outliers start: 32 outliers final: 12 residues processed: 276 average time/residue: 1.3831 time to fit residues: 436.2048 Evaluate side-chains 274 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 221 GLU Chi-restraints excluded: chain G residue 260 MET Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 176 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 21 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101984 restraints weight = 83888.797| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.88 r_work: 0.2952 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22016 Z= 0.098 Angle : 0.484 7.872 29960 Z= 0.255 Chirality : 0.044 0.147 3440 Planarity : 0.004 0.066 3928 Dihedral : 4.345 23.862 3048 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.50 % Allowed : 16.48 % Favored : 83.01 % 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: 0.57 (0.19), residues: 816 sheet: 0.39 (0.20), residues: 592 loop : -0.52 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 58 TYR 0.008 0.001 TYR C 339 PHE 0.006 0.001 PHE G 258 TRP 0.008 0.001 TRP C 352 HIS 0.003 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00232 (22016) covalent geometry : angle 0.48376 (29960) hydrogen bonds : bond 0.03686 ( 821) hydrogen bonds : angle 4.83641 ( 2196) *********************** 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 289 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 277 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8393 (t0) cc_final: 0.8148 (t0) REVERT: A 222 GLU cc_start: 0.8167 (tt0) cc_final: 0.7953 (tt0) REVERT: A 353 ASN cc_start: 0.8493 (t0) cc_final: 0.8282 (t0) REVERT: A 357 ASN cc_start: 0.8703 (m110) cc_final: 0.8250 (m110) REVERT: C 109 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: D 109 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: D 158 ASP cc_start: 0.8000 (t0) cc_final: 0.7631 (t0) REVERT: D 296 SER cc_start: 0.9051 (p) cc_final: 0.8789 (m) REVERT: E 110 TYR cc_start: 0.7541 (t80) cc_final: 0.7253 (t80) REVERT: E 220 ARG cc_start: 0.7311 (ttp80) cc_final: 0.6996 (tpt-90) REVERT: F 206 ASP cc_start: 0.7998 (m-30) cc_final: 0.7611 (m-30) REVERT: F 264 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8740 (mttt) REVERT: G 109 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: G 223 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7478 (ttm-80) REVERT: G 353 ASN cc_start: 0.8564 (t0) cc_final: 0.8336 (t0) outliers start: 12 outliers final: 5 residues processed: 285 average time/residue: 1.3813 time to fit residues: 449.9575 Evaluate side-chains 277 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 268 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain G residue 109 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 48 optimal weight: 0.0770 chunk 226 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.099346 restraints weight = 83981.651| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.95 r_work: 0.2966 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22016 Z= 0.162 Angle : 0.517 8.150 29960 Z= 0.275 Chirality : 0.046 0.151 3440 Planarity : 0.005 0.064 3928 Dihedral : 4.417 23.679 3048 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.80 % Allowed : 16.15 % Favored : 83.05 % 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: -0.15 (0.16), residues: 2768 helix: 0.46 (0.19), residues: 816 sheet: 0.32 (0.20), residues: 600 loop : -0.56 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 58 TYR 0.013 0.002 TYR E 339 PHE 0.009 0.001 PHE F 168 TRP 0.011 0.001 TRP C 352 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00394 (22016) covalent geometry : angle 0.51687 (29960) hydrogen bonds : bond 0.04253 ( 821) hydrogen bonds : angle 4.90855 ( 2196) *********************** 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 283 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 264 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8447 (t0) cc_final: 0.8192 (t0) REVERT: A 222 GLU cc_start: 0.8205 (tt0) cc_final: 0.7996 (tt0) REVERT: A 353 ASN cc_start: 0.8541 (t0) cc_final: 0.8336 (t0) REVERT: A 357 ASN cc_start: 0.8735 (m110) cc_final: 0.8318 (m110) REVERT: C 109 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: D 109 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8057 (pt0) REVERT: D 158 ASP cc_start: 0.8080 (t0) cc_final: 0.7718 (t0) REVERT: D 296 SER cc_start: 0.9034 (p) cc_final: 0.8806 (m) REVERT: E 220 ARG cc_start: 0.7364 (ttp80) cc_final: 0.7068 (tpt-90) REVERT: F 264 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8705 (mttt) REVERT: G 109 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7759 (pt0) REVERT: G 223 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7535 (ttm-80) REVERT: G 353 ASN cc_start: 0.8633 (t0) cc_final: 0.8414 (t0) outliers start: 19 outliers final: 8 residues processed: 276 average time/residue: 1.3743 time to fit residues: 435.3102 Evaluate side-chains 277 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 265 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain H residue 176 SER 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: 0.5980 chunk 101 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 137 optimal weight: 0.0980 chunk 139 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103257 restraints weight = 83363.346| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.89 r_work: 0.2981 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22016 Z= 0.087 Angle : 0.470 8.399 29960 Z= 0.245 Chirality : 0.044 0.146 3440 Planarity : 0.004 0.061 3928 Dihedral : 4.160 23.185 3048 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.34 % Allowed : 16.74 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2768 helix: 0.82 (0.20), residues: 816 sheet: 0.28 (0.20), residues: 584 loop : -0.28 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 220 TYR 0.007 0.001 TYR C 339 PHE 0.006 0.001 PHE G 258 TRP 0.013 0.001 TRP C 352 HIS 0.002 0.001 HIS G 100 Details of bonding type rmsd covalent geometry : bond 0.00205 (22016) covalent geometry : angle 0.47039 (29960) hydrogen bonds : bond 0.03315 ( 821) hydrogen bonds : angle 4.69111 ( 2196) ********************** 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 290 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 282 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8392 (t0) cc_final: 0.8147 (t0) REVERT: A 353 ASN cc_start: 0.8527 (t0) cc_final: 0.8321 (t0) REVERT: A 357 ASN cc_start: 0.8714 (m110) cc_final: 0.8282 (m110) REVERT: C 109 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: D 158 ASP cc_start: 0.8011 (t0) cc_final: 0.7628 (t0) REVERT: D 296 SER cc_start: 0.9013 (p) cc_final: 0.8745 (m) REVERT: E 220 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6974 (tpt-90) REVERT: F 206 ASP cc_start: 0.7973 (m-30) cc_final: 0.7612 (m-30) REVERT: F 264 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8666 (mttt) REVERT: G 223 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7465 (ttm-80) REVERT: G 353 ASN cc_start: 0.8598 (t0) cc_final: 0.8377 (t0) outliers start: 8 outliers final: 4 residues processed: 287 average time/residue: 1.2286 time to fit residues: 405.7875 Evaluate side-chains 274 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 268 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain F residue 264 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 167 optimal weight: 2.9990 chunk 251 optimal weight: 0.1980 chunk 234 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 268 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 353 ASN H 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102407 restraints weight = 83958.901| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.88 r_work: 0.2942 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22016 Z= 0.112 Angle : 0.483 9.387 29960 Z= 0.253 Chirality : 0.045 0.147 3440 Planarity : 0.004 0.059 3928 Dihedral : 4.157 22.762 3048 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.50 % Allowed : 16.65 % Favored : 82.84 % 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 (0.17), residues: 2768 helix: 0.82 (0.19), residues: 816 sheet: 0.31 (0.20), residues: 600 loop : -0.33 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 58 TYR 0.012 0.001 TYR H 110 PHE 0.006 0.001 PHE G 258 TRP 0.012 0.001 TRP C 352 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00272 (22016) covalent geometry : angle 0.48268 (29960) hydrogen bonds : bond 0.03635 ( 821) hydrogen bonds : angle 4.68291 ( 2196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11770.70 seconds wall clock time: 199 minutes 36.65 seconds (11976.65 seconds total)