Starting phenix.real_space_refine on Sat Jul 4 19:20:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s66_24851/07_2026/7s66_24851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s66_24851/07_2026/7s66_24851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s66_24851/07_2026/7s66_24851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s66_24851/07_2026/7s66_24851.map" model { file = "/net/cci-nas-00/data/ceres_data/7s66_24851/07_2026/7s66_24851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s66_24851/07_2026/7s66_24851.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s66_24851/07_2026/7s66_24851.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s66_24851/07_2026/7s66_24851.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 90 5.16 5 C 14540 2.51 5 N 4080 2.21 5 O 4484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23242 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3807 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 472} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3811 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 472} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, D, E, F Time building chain proxies: 4.62, per 1000 atoms: 0.20 Number of scatterers: 23242 At special positions: 0 Unit cell: (118.45, 118.45, 116.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 36 15.00 Mg 12 11.99 O 4484 8.00 N 4080 7.00 C 14540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 967.3 milliseconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 30 sheets defined 38.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.668A pdb=" N LEU A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.924A pdb=" N PHE A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 152' Processing helix chain 'A' and resid 156 through 175 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.570A pdb=" N MET A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.649A pdb=" N ALA A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 93 through 100 removed outlier: 3.668A pdb=" N LEU B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.924A pdb=" N PHE B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 152 " --> pdb=" O THR B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 152' Processing helix chain 'B' and resid 156 through 175 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 293 through 308 Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.569A pdb=" N MET B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.649A pdb=" N ALA B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 93 through 100 removed outlier: 3.669A pdb=" N LEU C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.924A pdb=" N PHE C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 152 " --> pdb=" O THR C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 152' Processing helix chain 'C' and resid 156 through 175 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 293 through 308 Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 334 through 341 removed outlier: 3.569A pdb=" N MET C 338 " --> pdb=" O ASP C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.649A pdb=" N ALA C 354 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 79 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 93 through 100 removed outlier: 3.668A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.924A pdb=" N PHE D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN D 152 " --> pdb=" O THR D 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 152' Processing helix chain 'D' and resid 156 through 175 Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 293 through 308 Processing helix chain 'D' and resid 320 through 330 Processing helix chain 'D' and resid 334 through 341 removed outlier: 3.570A pdb=" N MET D 338 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.649A pdb=" N ALA D 354 " --> pdb=" O PRO D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 51 through 67 Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 93 through 100 removed outlier: 3.668A pdb=" N LEU E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.924A pdb=" N PHE E 151 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN E 152 " --> pdb=" O THR E 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 147 through 152' Processing helix chain 'E' and resid 156 through 175 Processing helix chain 'E' and resid 196 through 201 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 293 through 308 Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 334 through 341 removed outlier: 3.570A pdb=" N MET E 338 " --> pdb=" O ASP E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.649A pdb=" N ALA E 354 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'E' and resid 379 through 384 Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 79 through 88 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 93 through 100 removed outlier: 3.668A pdb=" N LEU F 97 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 137 Processing helix chain 'F' and resid 147 through 152 removed outlier: 3.925A pdb=" N PHE F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN F 152 " --> pdb=" O THR F 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 147 through 152' Processing helix chain 'F' and resid 156 through 175 Processing helix chain 'F' and resid 196 through 201 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 267 through 274 Processing helix chain 'F' and resid 293 through 308 Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 334 through 341 removed outlier: 3.569A pdb=" N MET F 338 " --> pdb=" O ASP F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.649A pdb=" N ALA F 354 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 388 through 406 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.849A pdb=" N VAL A 142 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR A 181 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE A 144 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 203 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 12.880A pdb=" N ARG A 216 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N ILE A 239 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG A 218 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.410A pdb=" N ILE A 284 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASN A 414 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 286 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 12.711A pdb=" N MET A 449 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE A 472 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 451 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU A 469 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.849A pdb=" N VAL B 142 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR B 181 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 144 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 203 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 12.880A pdb=" N ARG B 216 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N ILE B 239 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG B 218 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA9, first strand: chain 'B' and resid 344 through 348 removed outlier: 6.410A pdb=" N ILE B 284 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASN B 414 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA B 286 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 12.711A pdb=" N MET B 449 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ILE B 472 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU B 469 " --> pdb=" O LYS B 480 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 486 through 487 Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 107 removed outlier: 6.849A pdb=" N VAL C 142 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR C 181 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 144 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 203 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 12.880A pdb=" N ARG C 216 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N ILE C 239 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG C 218 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AB5, first strand: chain 'C' and resid 344 through 348 removed outlier: 6.410A pdb=" N ILE C 284 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASN C 414 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA C 286 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 12.710A pdb=" N MET C 449 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE C 472 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU C 469 " --> pdb=" O LYS C 480 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AB7, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.849A pdb=" N VAL D 142 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR D 181 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE D 144 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 203 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 12.880A pdb=" N ARG D 216 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N ILE D 239 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG D 218 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 262 through 263 Processing sheet with id=AC1, first strand: chain 'D' and resid 344 through 348 removed outlier: 6.410A pdb=" N ILE D 284 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASN D 414 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA D 286 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 12.712A pdb=" N MET D 449 " --> pdb=" O ILE D 472 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE D 472 " --> pdb=" O MET D 449 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG D 451 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU D 469 " --> pdb=" O LYS D 480 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'E' and resid 103 through 107 removed outlier: 6.849A pdb=" N VAL E 142 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR E 181 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE E 144 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 203 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N ARG E 216 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N ILE E 239 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG E 218 " --> pdb=" O PHE E 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 262 through 263 Processing sheet with id=AC6, first strand: chain 'E' and resid 344 through 348 removed outlier: 6.410A pdb=" N ILE E 284 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASN E 414 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA E 286 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 12.712A pdb=" N MET E 449 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ILE E 472 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU E 469 " --> pdb=" O LYS E 480 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 486 through 487 Processing sheet with id=AC8, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC9, first strand: chain 'F' and resid 103 through 107 removed outlier: 6.849A pdb=" N VAL F 142 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR F 181 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE F 144 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 203 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 12.880A pdb=" N ARG F 216 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N ILE F 239 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG F 218 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 262 through 263 Processing sheet with id=AD2, first strand: chain 'F' and resid 344 through 348 removed outlier: 6.411A pdb=" N ILE F 284 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASN F 414 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA F 286 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 12.712A pdb=" N MET F 449 " --> pdb=" O ILE F 472 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE F 472 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU F 469 " --> pdb=" O LYS F 480 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 486 through 487 1092 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4799 1.32 - 1.45: 5403 1.45 - 1.57: 13220 1.57 - 1.69: 60 1.69 - 1.81: 162 Bond restraints: 23644 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP F 901 " pdb=" C5 ATP F 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C4 ATP C 901 " pdb=" C5 ATP C 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 ... (remaining 23639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 31568 4.41 - 8.82: 354 8.82 - 13.23: 12 13.23 - 17.64: 18 17.64 - 22.05: 6 Bond angle restraints: 31958 Sorted by residual: angle pdb=" PB ATP C 901 " pdb=" O3B ATP C 901 " pdb=" PG ATP C 901 " ideal model delta sigma weight residual 139.87 117.82 22.05 1.00e+00 1.00e+00 4.86e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 117.86 22.01 1.00e+00 1.00e+00 4.84e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 117.86 22.01 1.00e+00 1.00e+00 4.84e+02 angle pdb=" PB ATP F 901 " pdb=" O3B ATP F 901 " pdb=" PG ATP F 901 " ideal model delta sigma weight residual 139.87 117.88 21.99 1.00e+00 1.00e+00 4.84e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 117.88 21.99 1.00e+00 1.00e+00 4.84e+02 ... (remaining 31953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 13448 17.48 - 34.97: 442 34.97 - 52.45: 96 52.45 - 69.93: 36 69.93 - 87.41: 12 Dihedral angle restraints: 14034 sinusoidal: 5718 harmonic: 8316 Sorted by residual: dihedral pdb=" CA TYR F 154 " pdb=" C TYR F 154 " pdb=" N ASP F 155 " pdb=" CA ASP F 155 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR A 154 " pdb=" C TYR A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR E 154 " pdb=" C TYR E 154 " pdb=" N ASP E 155 " pdb=" CA ASP E 155 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 14031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2015 0.048 - 0.095: 1082 0.095 - 0.143: 364 0.143 - 0.191: 73 0.191 - 0.238: 24 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CA TRP E 92 " pdb=" N TRP E 92 " pdb=" C TRP E 92 " pdb=" CB TRP E 92 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA TRP F 92 " pdb=" N TRP F 92 " pdb=" C TRP F 92 " pdb=" CB TRP F 92 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA TRP C 92 " pdb=" N TRP C 92 " pdb=" C TRP C 92 " pdb=" CB TRP C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 3555 not shown) Planarity restraints: 4090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 92 " -0.083 2.00e-02 2.50e+03 4.15e-02 4.30e+01 pdb=" CG TRP B 92 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP B 92 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 92 " 0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP B 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 92 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 92 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 92 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 92 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 92 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 92 " 0.083 2.00e-02 2.50e+03 4.15e-02 4.30e+01 pdb=" CG TRP C 92 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 92 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 92 " -0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP C 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 92 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP C 92 " -0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 92 " 0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 92 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 92 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 92 " -0.082 2.00e-02 2.50e+03 4.14e-02 4.28e+01 pdb=" CG TRP A 92 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 92 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 92 " 0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP A 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 92 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 92 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 92 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 92 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 92 " -0.037 2.00e-02 2.50e+03 ... (remaining 4087 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 42 2.40 - 3.02: 13703 3.02 - 3.65: 33865 3.65 - 4.27: 56328 4.27 - 4.90: 93135 Nonbonded interactions: 197073 Sorted by model distance: nonbonded pdb=" OG1 THR F 53 " pdb="MG MG F 904 " model vdw 1.770 2.170 nonbonded pdb=" OG1 THR D 53 " pdb="MG MG D 904 " model vdw 1.770 2.170 nonbonded pdb=" OG1 THR E 53 " pdb="MG MG E 904 " model vdw 1.771 2.170 nonbonded pdb=" OG1 THR A 53 " pdb="MG MG A 904 " model vdw 1.771 2.170 nonbonded pdb=" OG1 THR C 53 " pdb="MG MG C 904 " model vdw 1.771 2.170 ... (remaining 197068 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.022 0.810 23656 Z= 1.877 Angle : 1.344 22.048 31958 Z= 1.009 Chirality : 0.063 0.238 3558 Planarity : 0.010 0.042 4090 Dihedral : 10.544 87.414 8694 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.50 (0.15), residues: 2898 helix: 0.06 (0.14), residues: 1038 sheet: 0.80 (0.20), residues: 774 loop : 0.53 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 161 TYR 0.064 0.013 TYR E 235 PHE 0.050 0.009 PHE F 237 TRP 0.083 0.016 TRP B 92 HIS 0.007 0.002 HIS D 423 Details of bonding type rmsd/Z covalent geometry : bond 0.01289 / 0.74 (23644) covalent geometry : angle 1.34395 / 1.01 (31958) hydrogen bonds : bond 0.16213 / 10.85 ( 1092) hydrogen bonds : angle 6.91616 / 4.92 ( 3060) Misc. bond : bond 0.76545 / 43.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.893 Fit side-chains REVERT: A 235 TYR cc_start: 0.8981 (m-80) cc_final: 0.8648 (m-80) REVERT: A 404 LYS cc_start: 0.8205 (mttt) cc_final: 0.7994 (mttm) REVERT: B 487 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7185 (mt-10) REVERT: C 487 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7090 (mm-30) REVERT: D 235 TYR cc_start: 0.8987 (m-80) cc_final: 0.8649 (m-80) REVERT: D 273 MET cc_start: 0.8715 (mtp) cc_final: 0.8481 (mtm) REVERT: E 281 ASP cc_start: 0.7122 (m-30) cc_final: 0.6610 (m-30) REVERT: E 362 ILE cc_start: 0.8826 (mt) cc_final: 0.8580 (mp) REVERT: E 487 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7192 (mt-10) REVERT: F 487 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7121 (mm-30) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.7569 time to fit residues: 516.7679 Evaluate side-chains 319 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111083 restraints weight = 27852.723| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.15 r_work: 0.3236 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23656 Z= 0.136 Angle : 0.510 5.701 31958 Z= 0.285 Chirality : 0.043 0.135 3558 Planarity : 0.004 0.030 4090 Dihedral : 5.908 77.834 3240 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.74 % Allowed : 10.79 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.15), residues: 2898 helix: 1.39 (0.16), residues: 1044 sheet: 0.41 (0.19), residues: 780 loop : 0.33 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 340 TYR 0.016 0.002 TYR B 154 PHE 0.021 0.002 PHE A 301 TRP 0.032 0.003 TRP C 92 HIS 0.004 0.001 HIS F 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (23644) covalent geometry : angle 0.50990 / 0.29 (31958) hydrogen bonds : bond 0.04081 / 2.72 ( 1092) hydrogen bonds : angle 4.80167 / 3.40 ( 3060) Misc. bond : bond 0.00270 / 0.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 349 time to evaluate : 0.863 Fit side-chains REVERT: A 336 GLU cc_start: 0.7999 (tp30) cc_final: 0.7752 (tt0) REVERT: A 357 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: A 393 ARG cc_start: 0.7266 (mtm110) cc_final: 0.6909 (mtm110) REVERT: A 404 LYS cc_start: 0.7877 (mttt) cc_final: 0.7537 (mttm) REVERT: A 426 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7780 (t) REVERT: B 128 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 357 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: B 471 MET cc_start: 0.8347 (mpp) cc_final: 0.7996 (mpp) REVERT: B 480 LYS cc_start: 0.7987 (mttp) cc_final: 0.7636 (mttp) REVERT: B 487 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6976 (mt-10) REVERT: C 81 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: C 393 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6756 (mtm110) REVERT: C 426 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8031 (t) REVERT: C 448 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7122 (mt-10) REVERT: C 487 GLU cc_start: 0.7624 (mt-10) cc_final: 0.6899 (mt-10) REVERT: D 336 GLU cc_start: 0.7811 (tt0) cc_final: 0.7441 (tt0) REVERT: D 357 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: D 393 ARG cc_start: 0.7213 (mtm110) cc_final: 0.6851 (mtm110) REVERT: D 426 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7820 (t) REVERT: D 471 MET cc_start: 0.8446 (mpp) cc_final: 0.8204 (mpp) REVERT: E 257 ARG cc_start: 0.7139 (mmt180) cc_final: 0.6891 (mtm-85) REVERT: E 362 ILE cc_start: 0.8547 (mt) cc_final: 0.8115 (mp) REVERT: E 480 LYS cc_start: 0.7985 (mttp) cc_final: 0.7685 (mttp) REVERT: E 487 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6975 (mt-10) REVERT: E 488 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7337 (mtm110) REVERT: F 81 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: F 253 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7331 (mmp80) REVERT: F 366 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: F 393 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6772 (mtm110) REVERT: F 407 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7545 (mm-30) REVERT: F 448 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7147 (mt-10) REVERT: F 487 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6960 (mt-10) outliers start: 67 outliers final: 14 residues processed: 406 average time/residue: 0.6257 time to fit residues: 288.4549 Evaluate side-chains 316 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 290 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 253 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 174 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 233 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 361 GLN E 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108887 restraints weight = 28928.233| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.05 r_work: 0.3162 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.052 23656 Z= 0.372 Angle : 0.659 7.644 31958 Z= 0.352 Chirality : 0.050 0.295 3558 Planarity : 0.005 0.037 4090 Dihedral : 6.200 80.065 3240 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.80 % Allowed : 11.08 % Favored : 85.12 % 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: 0.38 (0.15), residues: 2898 helix: 1.10 (0.16), residues: 1080 sheet: -0.05 (0.18), residues: 774 loop : -0.24 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 340 TYR 0.019 0.003 TYR B 235 PHE 0.033 0.004 PHE C 301 TRP 0.038 0.004 TRP E 92 HIS 0.009 0.002 HIS E 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.37 (23644) covalent geometry : angle 0.65933 / 0.35 (31958) hydrogen bonds : bond 0.04883 / 3.31 ( 1092) hydrogen bonds : angle 4.85508 / 3.44 ( 3060) Misc. bond : bond 0.00411 / 0.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 302 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7468 (pt0) REVERT: A 162 ARG cc_start: 0.7788 (ttp-170) cc_final: 0.7563 (ttp80) REVERT: A 336 GLU cc_start: 0.8200 (tp30) cc_final: 0.7865 (tt0) REVERT: A 404 LYS cc_start: 0.7987 (mttt) cc_final: 0.7657 (mttm) REVERT: B 128 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 247 PHE cc_start: 0.7543 (m-80) cc_final: 0.7137 (t80) REVERT: B 362 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8559 (mp) REVERT: B 449 MET cc_start: 0.9119 (mtp) cc_final: 0.8832 (mtp) REVERT: B 471 MET cc_start: 0.8494 (mpp) cc_final: 0.8106 (mpp) REVERT: B 480 LYS cc_start: 0.8475 (mttp) cc_final: 0.8105 (mttm) REVERT: B 487 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7558 (mt-10) REVERT: C 128 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7557 (mm-30) REVERT: C 217 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8058 (ttt90) REVERT: C 393 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7186 (mtm110) REVERT: C 487 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7457 (mt-10) REVERT: D 77 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7490 (pt0) REVERT: D 162 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7545 (ttp80) REVERT: D 235 TYR cc_start: 0.9121 (m-80) cc_final: 0.8794 (m-80) REVERT: D 336 GLU cc_start: 0.8037 (tt0) cc_final: 0.7622 (tt0) REVERT: E 128 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7615 (mm-30) REVERT: E 247 PHE cc_start: 0.7528 (m-80) cc_final: 0.7132 (t80) REVERT: E 257 ARG cc_start: 0.7361 (mmt180) cc_final: 0.7103 (mtm-85) REVERT: E 362 ILE cc_start: 0.8836 (mt) cc_final: 0.8397 (mp) REVERT: E 471 MET cc_start: 0.8489 (mpp) cc_final: 0.8152 (mpp) REVERT: E 480 LYS cc_start: 0.8451 (mttp) cc_final: 0.8165 (mttm) REVERT: E 487 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7513 (mt-10) REVERT: F 124 SER cc_start: 0.7621 (m) cc_final: 0.7100 (t) REVERT: F 128 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7540 (mm-30) REVERT: F 217 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8102 (ttt90) REVERT: F 333 MET cc_start: 0.8199 (mtp) cc_final: 0.7894 (mtp) REVERT: F 357 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: F 366 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: F 393 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7190 (mtm110) REVERT: F 480 LYS cc_start: 0.8428 (mttp) cc_final: 0.8182 (mttm) REVERT: F 487 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7366 (mt-10) outliers start: 93 outliers final: 48 residues processed: 380 average time/residue: 0.6588 time to fit residues: 281.2122 Evaluate side-chains 313 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 100 optimal weight: 0.9980 chunk 217 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112823 restraints weight = 28778.147| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.06 r_work: 0.3239 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23656 Z= 0.097 Angle : 0.432 5.595 31958 Z= 0.239 Chirality : 0.041 0.174 3558 Planarity : 0.003 0.040 4090 Dihedral : 5.975 88.432 3240 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.41 % Allowed : 13.74 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 2898 helix: 1.53 (0.16), residues: 1080 sheet: 0.07 (0.19), residues: 756 loop : -0.31 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 340 TYR 0.013 0.001 TYR A 154 PHE 0.018 0.001 PHE C 301 TRP 0.027 0.002 TRP A 92 HIS 0.002 0.000 HIS E 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (23644) covalent geometry : angle 0.43226 / 0.24 (31958) hydrogen bonds : bond 0.03087 / 2.06 ( 1092) hydrogen bonds : angle 4.38064 / 3.09 ( 3060) Misc. bond : bond 0.00092 / 0.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 332 time to evaluate : 0.627 Fit side-chains REVERT: A 77 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7406 (pt0) REVERT: A 162 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.7406 (ttp80) REVERT: A 269 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7382 (tmt170) REVERT: A 310 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: A 336 GLU cc_start: 0.8168 (tp30) cc_final: 0.7839 (tt0) REVERT: A 358 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: A 404 LYS cc_start: 0.8046 (mttt) cc_final: 0.7730 (mttm) REVERT: A 461 SER cc_start: 0.9187 (t) cc_final: 0.8923 (p) REVERT: A 488 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7157 (mtm-85) REVERT: B 128 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7684 (mm-30) REVERT: B 150 VAL cc_start: 0.8002 (m) cc_final: 0.7777 (p) REVERT: B 247 PHE cc_start: 0.7479 (m-80) cc_final: 0.6940 (t80) REVERT: B 357 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: B 362 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8668 (mp) REVERT: B 471 MET cc_start: 0.8432 (mpp) cc_final: 0.8079 (mpp) REVERT: B 480 LYS cc_start: 0.8448 (mttp) cc_final: 0.8157 (mttp) REVERT: B 487 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7368 (mt-10) REVERT: C 81 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: C 128 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7573 (mm-30) REVERT: C 357 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: C 393 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7032 (mtm110) REVERT: C 431 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: C 487 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7169 (mt-10) REVERT: D 77 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7405 (pt0) REVERT: D 162 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.7459 (ttp80) REVERT: D 269 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7373 (tmt170) REVERT: D 310 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: D 336 GLU cc_start: 0.8088 (tt0) cc_final: 0.7595 (tt0) REVERT: D 358 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: D 362 ILE cc_start: 0.8756 (mm) cc_final: 0.8434 (mp) REVERT: D 461 SER cc_start: 0.9185 (t) cc_final: 0.8926 (p) REVERT: E 150 VAL cc_start: 0.7998 (m) cc_final: 0.7769 (p) REVERT: E 247 PHE cc_start: 0.7474 (m-80) cc_final: 0.6935 (t80) REVERT: E 362 ILE cc_start: 0.8914 (mt) cc_final: 0.8517 (mp) REVERT: F 81 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.8008 (mp10) REVERT: F 128 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7520 (mm-30) REVERT: F 357 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: F 393 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7025 (mtm110) REVERT: F 487 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7149 (mt-10) outliers start: 59 outliers final: 17 residues processed: 384 average time/residue: 0.6766 time to fit residues: 292.1956 Evaluate side-chains 311 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 65 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109849 restraints weight = 28666.950| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.03 r_work: 0.3177 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 23656 Z= 0.235 Angle : 0.534 6.807 31958 Z= 0.287 Chirality : 0.045 0.243 3558 Planarity : 0.004 0.048 4090 Dihedral : 5.926 79.647 3240 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.39 % Allowed : 14.15 % Favored : 82.46 % 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: 0.51 (0.15), residues: 2898 helix: 1.48 (0.16), residues: 1080 sheet: -0.05 (0.18), residues: 756 loop : -0.44 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 340 TYR 0.014 0.002 TYR B 235 PHE 0.028 0.002 PHE F 301 TRP 0.031 0.003 TRP C 92 HIS 0.009 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.23 (23644) covalent geometry : angle 0.53398 / 0.29 (31958) hydrogen bonds : bond 0.03820 / 2.60 ( 1092) hydrogen bonds : angle 4.44682 / 3.15 ( 3060) Misc. bond : bond 0.00356 / 0.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 280 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7470 (pt0) REVERT: A 162 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7427 (ttp80) REVERT: A 269 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7434 (tmt170) REVERT: A 310 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: A 336 GLU cc_start: 0.8264 (tp30) cc_final: 0.7862 (tt0) REVERT: A 404 LYS cc_start: 0.7973 (mttt) cc_final: 0.7612 (mttm) REVERT: A 461 SER cc_start: 0.9319 (t) cc_final: 0.9029 (p) REVERT: B 128 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 150 VAL cc_start: 0.8051 (m) cc_final: 0.7774 (p) REVERT: B 247 PHE cc_start: 0.7726 (m-80) cc_final: 0.7061 (t80) REVERT: B 357 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: B 362 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8617 (mp) REVERT: B 471 MET cc_start: 0.8543 (mpp) cc_final: 0.8157 (mpp) REVERT: B 480 LYS cc_start: 0.8409 (mttp) cc_final: 0.8034 (mttp) REVERT: B 487 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7554 (mt-10) REVERT: C 106 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8376 (tt) REVERT: C 128 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7523 (mm-30) REVERT: C 150 VAL cc_start: 0.7982 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 357 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: C 393 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7060 (mtm110) REVERT: C 431 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: C 487 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7313 (mt-10) REVERT: D 77 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7468 (pt0) REVERT: D 162 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.7422 (ttp80) REVERT: D 269 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7471 (tmt170) REVERT: D 310 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: D 336 GLU cc_start: 0.8096 (tt0) cc_final: 0.7561 (tt0) REVERT: D 461 SER cc_start: 0.9327 (t) cc_final: 0.9040 (p) REVERT: D 480 LYS cc_start: 0.8188 (mttp) cc_final: 0.7869 (mttm) REVERT: E 57 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8689 (mm) REVERT: E 247 PHE cc_start: 0.7719 (m-80) cc_final: 0.7057 (t80) REVERT: E 362 ILE cc_start: 0.8814 (mt) cc_final: 0.8484 (mp) REVERT: E 471 MET cc_start: 0.8435 (mpp) cc_final: 0.8097 (mpt) REVERT: E 487 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7495 (mt-10) REVERT: F 128 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7515 (mm-30) REVERT: F 150 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7760 (p) REVERT: F 357 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: F 393 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7037 (mtm110) REVERT: F 431 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: F 471 MET cc_start: 0.8461 (mpp) cc_final: 0.8222 (pmm) REVERT: F 480 LYS cc_start: 0.8369 (mttp) cc_final: 0.8083 (mttp) REVERT: F 487 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7287 (mt-10) outliers start: 83 outliers final: 44 residues processed: 350 average time/residue: 0.7034 time to fit residues: 276.3330 Evaluate side-chains 325 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 431 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112700 restraints weight = 28644.548| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.03 r_work: 0.3226 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23656 Z= 0.099 Angle : 0.420 5.129 31958 Z= 0.230 Chirality : 0.041 0.164 3558 Planarity : 0.003 0.037 4090 Dihedral : 5.865 87.772 3240 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 14.76 % Favored : 82.34 % 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: 0.80 (0.16), residues: 2898 helix: 1.80 (0.16), residues: 1074 sheet: 0.08 (0.19), residues: 756 loop : -0.35 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 140 TYR 0.010 0.001 TYR A 154 PHE 0.016 0.001 PHE F 301 TRP 0.024 0.002 TRP C 92 HIS 0.003 0.000 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (23644) covalent geometry : angle 0.42039 / 0.23 (31958) hydrogen bonds : bond 0.02862 / 1.93 ( 1092) hydrogen bonds : angle 4.18694 / 2.96 ( 3060) Misc. bond : bond 0.00069 / 0.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 296 time to evaluate : 0.791 Fit side-chains REVERT: A 77 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7486 (pt0) REVERT: A 162 ARG cc_start: 0.7599 (ttp-170) cc_final: 0.7395 (ttp80) REVERT: A 336 GLU cc_start: 0.8110 (tp30) cc_final: 0.7800 (tt0) REVERT: A 362 ILE cc_start: 0.8560 (mm) cc_final: 0.8336 (mp) REVERT: A 404 LYS cc_start: 0.8074 (mttt) cc_final: 0.7742 (mttm) REVERT: A 461 SER cc_start: 0.9198 (t) cc_final: 0.8950 (p) REVERT: B 128 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 150 VAL cc_start: 0.8134 (m) cc_final: 0.7861 (p) REVERT: B 247 PHE cc_start: 0.7528 (m-80) cc_final: 0.7008 (t80) REVERT: B 357 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: B 362 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8699 (mp) REVERT: B 471 MET cc_start: 0.8430 (mpp) cc_final: 0.8015 (mpp) REVERT: B 480 LYS cc_start: 0.8394 (mttp) cc_final: 0.8054 (mttp) REVERT: B 488 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7614 (mtm-85) REVERT: C 106 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8492 (tt) REVERT: C 128 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7581 (mm-30) REVERT: C 147 VAL cc_start: 0.8774 (m) cc_final: 0.8550 (m) REVERT: C 150 VAL cc_start: 0.7790 (m) cc_final: 0.7494 (p) REVERT: C 357 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: C 393 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7037 (mtm110) REVERT: C 487 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7237 (mt-10) REVERT: D 77 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7487 (pt0) REVERT: D 162 ARG cc_start: 0.7624 (ttp-170) cc_final: 0.7411 (ttp80) REVERT: D 269 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7544 (tmt170) REVERT: D 336 GLU cc_start: 0.8079 (tt0) cc_final: 0.7583 (tt0) REVERT: D 362 ILE cc_start: 0.8551 (mm) cc_final: 0.8305 (mp) REVERT: D 461 SER cc_start: 0.9141 (t) cc_final: 0.8878 (p) REVERT: E 162 ARG cc_start: 0.7591 (ttp80) cc_final: 0.7087 (ttp80) REVERT: E 247 PHE cc_start: 0.7531 (m-80) cc_final: 0.7018 (t80) REVERT: E 257 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7583 (mtm-85) REVERT: E 362 ILE cc_start: 0.8922 (mt) cc_final: 0.8549 (mp) REVERT: E 461 SER cc_start: 0.9320 (t) cc_final: 0.9098 (p) REVERT: E 471 MET cc_start: 0.8365 (mpp) cc_final: 0.7858 (mpt) REVERT: E 488 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7532 (mtm-85) REVERT: F 106 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8503 (tt) REVERT: F 124 SER cc_start: 0.7644 (m) cc_final: 0.7124 (t) REVERT: F 128 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7539 (mm-30) REVERT: F 147 VAL cc_start: 0.8693 (m) cc_final: 0.8475 (m) REVERT: F 150 VAL cc_start: 0.7798 (m) cc_final: 0.7501 (p) REVERT: F 357 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: F 393 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7009 (mtm110) REVERT: F 431 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: F 471 MET cc_start: 0.8377 (mpp) cc_final: 0.8132 (pmm) REVERT: F 480 LYS cc_start: 0.8198 (mttm) cc_final: 0.7950 (mttp) REVERT: F 487 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7204 (mt-10) outliers start: 71 outliers final: 29 residues processed: 354 average time/residue: 0.6801 time to fit residues: 270.5675 Evaluate side-chains 317 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 431 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 249 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 283 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110157 restraints weight = 29013.899| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.05 r_work: 0.3196 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23656 Z= 0.159 Angle : 0.469 6.245 31958 Z= 0.253 Chirality : 0.043 0.182 3558 Planarity : 0.003 0.041 4090 Dihedral : 5.824 83.787 3240 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.58 % Allowed : 15.62 % Favored : 81.81 % 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: 0.77 (0.15), residues: 2898 helix: 1.80 (0.16), residues: 1074 sheet: 0.09 (0.19), residues: 756 loop : -0.41 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 140 TYR 0.011 0.002 TYR C 235 PHE 0.022 0.002 PHE F 301 TRP 0.024 0.002 TRP A 92 HIS 0.003 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (23644) covalent geometry : angle 0.46888 / 0.25 (31958) hydrogen bonds : bond 0.03195 / 2.17 ( 1092) hydrogen bonds : angle 4.19721 / 2.96 ( 3060) Misc. bond : bond 0.00185 / 0.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.589 Fit side-chains REVERT: A 77 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7378 (pt0) REVERT: A 162 ARG cc_start: 0.7602 (ttp-170) cc_final: 0.7401 (ttp80) REVERT: A 336 GLU cc_start: 0.8191 (tp30) cc_final: 0.7836 (tt0) REVERT: A 357 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: A 390 ASN cc_start: 0.8496 (m-40) cc_final: 0.8249 (m110) REVERT: A 404 LYS cc_start: 0.8070 (mttt) cc_final: 0.7733 (mttm) REVERT: A 461 SER cc_start: 0.9233 (t) cc_final: 0.8959 (p) REVERT: B 128 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 150 VAL cc_start: 0.8149 (m) cc_final: 0.7871 (p) REVERT: B 247 PHE cc_start: 0.7654 (m-80) cc_final: 0.7092 (t80) REVERT: B 357 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 362 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 471 MET cc_start: 0.8433 (mpp) cc_final: 0.8091 (mpp) REVERT: B 480 LYS cc_start: 0.8379 (mttp) cc_final: 0.8025 (mttp) REVERT: B 487 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7533 (mt-10) REVERT: B 488 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7596 (mtm-85) REVERT: C 106 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8514 (tt) REVERT: C 128 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7578 (mm-30) REVERT: C 147 VAL cc_start: 0.8824 (m) cc_final: 0.8593 (m) REVERT: C 150 VAL cc_start: 0.7839 (m) cc_final: 0.7521 (p) REVERT: C 357 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: C 393 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6988 (mtm110) REVERT: C 487 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7284 (mt-10) REVERT: D 77 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7410 (pt0) REVERT: D 88 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7664 (tpp80) REVERT: D 162 ARG cc_start: 0.7616 (ttp-170) cc_final: 0.7406 (ttp80) REVERT: D 269 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7524 (tmt170) REVERT: D 336 GLU cc_start: 0.8089 (tt0) cc_final: 0.7590 (tt0) REVERT: D 357 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: D 390 ASN cc_start: 0.8518 (m-40) cc_final: 0.8282 (m110) REVERT: D 461 SER cc_start: 0.9235 (t) cc_final: 0.8965 (p) REVERT: E 247 PHE cc_start: 0.7648 (m-80) cc_final: 0.7083 (t80) REVERT: E 257 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7554 (mtm-85) REVERT: E 362 ILE cc_start: 0.8864 (mt) cc_final: 0.8554 (mt) REVERT: E 471 MET cc_start: 0.8397 (mpp) cc_final: 0.8165 (mpp) REVERT: E 488 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7527 (mtm-85) REVERT: F 106 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8384 (tt) REVERT: F 124 SER cc_start: 0.7635 (m) cc_final: 0.7112 (t) REVERT: F 128 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7494 (mm-30) REVERT: F 147 VAL cc_start: 0.8836 (m) cc_final: 0.8618 (m) REVERT: F 150 VAL cc_start: 0.7851 (m) cc_final: 0.7538 (p) REVERT: F 357 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: F 393 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6986 (mtm110) REVERT: F 431 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: F 471 MET cc_start: 0.8420 (mpp) cc_final: 0.8118 (mpp) REVERT: F 480 LYS cc_start: 0.8194 (mttm) cc_final: 0.7786 (mttp) REVERT: F 487 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7242 (mt-10) outliers start: 63 outliers final: 29 residues processed: 333 average time/residue: 0.7005 time to fit residues: 261.1978 Evaluate side-chains 317 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 281 optimal weight: 5.9990 chunk 278 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 250 optimal weight: 40.0000 chunk 123 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109028 restraints weight = 28890.589| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.04 r_work: 0.3178 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23656 Z= 0.179 Angle : 0.480 5.693 31958 Z= 0.258 Chirality : 0.043 0.191 3558 Planarity : 0.003 0.040 4090 Dihedral : 5.830 81.724 3240 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.49 % Allowed : 15.90 % Favored : 81.60 % 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: 0.69 (0.15), residues: 2898 helix: 1.76 (0.16), residues: 1074 sheet: 0.02 (0.19), residues: 756 loop : -0.47 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 140 TYR 0.012 0.002 TYR C 235 PHE 0.023 0.002 PHE F 301 TRP 0.024 0.002 TRP A 92 HIS 0.003 0.001 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (23644) covalent geometry : angle 0.48031 / 0.26 (31958) hydrogen bonds : bond 0.03309 / 2.25 ( 1092) hydrogen bonds : angle 4.22859 / 2.98 ( 3060) Misc. bond : bond 0.00204 / 0.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 290 time to evaluate : 0.826 Fit side-chains REVERT: A 77 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7409 (pt0) REVERT: A 88 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7774 (tpp80) REVERT: A 162 ARG cc_start: 0.7611 (ttp-170) cc_final: 0.7405 (ttp80) REVERT: A 336 GLU cc_start: 0.8208 (tp30) cc_final: 0.7863 (tt0) REVERT: A 357 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: A 390 ASN cc_start: 0.8527 (m-40) cc_final: 0.8293 (m110) REVERT: A 404 LYS cc_start: 0.8065 (mttt) cc_final: 0.7725 (mttm) REVERT: A 461 SER cc_start: 0.9242 (t) cc_final: 0.8976 (p) REVERT: B 128 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7652 (mm-30) REVERT: B 150 VAL cc_start: 0.8066 (m) cc_final: 0.7797 (p) REVERT: B 247 PHE cc_start: 0.7682 (m-80) cc_final: 0.7124 (t80) REVERT: B 357 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: B 362 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8479 (mp) REVERT: B 471 MET cc_start: 0.8407 (mpp) cc_final: 0.8063 (mpp) REVERT: B 480 LYS cc_start: 0.8402 (mttp) cc_final: 0.8039 (mttm) REVERT: B 487 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 488 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7577 (mtm-85) REVERT: C 106 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8387 (tt) REVERT: C 128 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 150 VAL cc_start: 0.7784 (m) cc_final: 0.7461 (p) REVERT: C 357 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: C 393 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7024 (mtm110) REVERT: C 487 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7317 (mt-10) REVERT: D 77 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7425 (pt0) REVERT: D 88 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7785 (tpp80) REVERT: D 162 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7430 (ttp80) REVERT: D 232 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.7717 (mmtt) REVERT: D 269 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7472 (tmt170) REVERT: D 336 GLU cc_start: 0.8068 (tt0) cc_final: 0.7559 (tt0) REVERT: D 357 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: D 390 ASN cc_start: 0.8516 (m-40) cc_final: 0.8285 (m110) REVERT: D 461 SER cc_start: 0.9236 (t) cc_final: 0.8977 (p) REVERT: E 247 PHE cc_start: 0.7681 (m-80) cc_final: 0.7129 (t80) REVERT: E 362 ILE cc_start: 0.8895 (mt) cc_final: 0.8589 (mt) REVERT: E 487 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7512 (mt-10) REVERT: E 488 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7545 (mtm-85) REVERT: F 54 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8590 (tt) REVERT: F 106 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8392 (tt) REVERT: F 124 SER cc_start: 0.7637 (m) cc_final: 0.7090 (t) REVERT: F 128 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7515 (mm-30) REVERT: F 150 VAL cc_start: 0.7800 (m) cc_final: 0.7481 (p) REVERT: F 357 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: F 393 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6991 (mtm110) REVERT: F 431 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: F 471 MET cc_start: 0.8448 (mpp) cc_final: 0.8168 (mpp) REVERT: F 480 LYS cc_start: 0.8155 (mttm) cc_final: 0.7771 (mttp) REVERT: F 487 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7313 (mt-10) outliers start: 61 outliers final: 35 residues processed: 339 average time/residue: 0.6816 time to fit residues: 259.8445 Evaluate side-chains 328 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 431 GLU Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 56 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111403 restraints weight = 28935.678| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.04 r_work: 0.3211 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23656 Z= 0.115 Angle : 0.434 4.898 31958 Z= 0.235 Chirality : 0.041 0.157 3558 Planarity : 0.003 0.035 4090 Dihedral : 5.785 85.956 3240 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.25 % Allowed : 16.31 % Favored : 81.44 % 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: 0.81 (0.16), residues: 2898 helix: 1.89 (0.16), residues: 1074 sheet: -0.01 (0.18), residues: 780 loop : -0.36 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 140 TYR 0.010 0.001 TYR C 235 PHE 0.018 0.001 PHE F 301 TRP 0.024 0.002 TRP A 92 HIS 0.003 0.000 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (23644) covalent geometry : angle 0.43389 / 0.24 (31958) hydrogen bonds : bond 0.02893 / 1.96 ( 1092) hydrogen bonds : angle 4.11858 / 2.91 ( 3060) Misc. bond : bond 0.00119 / 0.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 288 time to evaluate : 0.701 Fit side-chains REVERT: A 77 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7383 (pt0) REVERT: A 232 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.7752 (mmtt) REVERT: A 336 GLU cc_start: 0.8109 (tp30) cc_final: 0.7793 (tt0) REVERT: A 357 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: A 362 ILE cc_start: 0.8514 (mm) cc_final: 0.8302 (mp) REVERT: A 390 ASN cc_start: 0.8514 (m-40) cc_final: 0.8280 (m110) REVERT: A 404 LYS cc_start: 0.8048 (mttt) cc_final: 0.7715 (mttm) REVERT: A 461 SER cc_start: 0.9186 (t) cc_final: 0.8936 (p) REVERT: B 128 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7707 (mm-30) REVERT: B 150 VAL cc_start: 0.8098 (m) cc_final: 0.7813 (p) REVERT: B 247 PHE cc_start: 0.7599 (m-80) cc_final: 0.7056 (t80) REVERT: B 357 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: B 362 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8473 (mp) REVERT: B 461 SER cc_start: 0.9330 (t) cc_final: 0.9111 (p) REVERT: B 471 MET cc_start: 0.8425 (mpp) cc_final: 0.8025 (mpp) REVERT: B 480 LYS cc_start: 0.8351 (mttp) cc_final: 0.7994 (mttm) REVERT: B 487 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 488 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7629 (mtm-85) REVERT: C 106 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8494 (tt) REVERT: C 128 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7639 (mm-30) REVERT: C 150 VAL cc_start: 0.7782 (m) cc_final: 0.7422 (p) REVERT: C 357 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7510 (pt0) REVERT: C 393 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7025 (mtm110) REVERT: C 487 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7316 (mt-10) REVERT: D 77 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7424 (pt0) REVERT: D 162 ARG cc_start: 0.7579 (ttp-170) cc_final: 0.7378 (ttp80) REVERT: D 232 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.7753 (mmtt) REVERT: D 336 GLU cc_start: 0.8063 (tt0) cc_final: 0.7547 (tt0) REVERT: D 357 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: D 390 ASN cc_start: 0.8515 (m-40) cc_final: 0.8281 (m110) REVERT: D 461 SER cc_start: 0.9194 (t) cc_final: 0.8958 (p) REVERT: E 247 PHE cc_start: 0.7602 (m-80) cc_final: 0.7068 (t80) REVERT: E 362 ILE cc_start: 0.8903 (mt) cc_final: 0.8532 (mt) REVERT: E 488 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7627 (mtm-85) REVERT: F 54 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8573 (tt) REVERT: F 106 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8502 (tt) REVERT: F 124 SER cc_start: 0.7651 (m) cc_final: 0.7118 (t) REVERT: F 128 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7608 (mm-30) REVERT: F 150 VAL cc_start: 0.7767 (m) cc_final: 0.7446 (p) REVERT: F 357 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7532 (pt0) REVERT: F 393 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7008 (mtm110) REVERT: F 487 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7310 (mt-10) outliers start: 55 outliers final: 31 residues processed: 338 average time/residue: 0.6676 time to fit residues: 254.4561 Evaluate side-chains 324 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 471 MET Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 67 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 142 optimal weight: 0.0020 chunk 235 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 chunk 166 optimal weight: 0.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110237 restraints weight = 28954.449| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.04 r_work: 0.3198 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 23656 Z= 0.149 Angle : 0.454 5.081 31958 Z= 0.246 Chirality : 0.042 0.175 3558 Planarity : 0.003 0.055 4090 Dihedral : 5.780 85.002 3240 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.96 % Allowed : 16.64 % Favored : 81.40 % 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: 0.79 (0.15), residues: 2898 helix: 1.89 (0.16), residues: 1074 sheet: -0.02 (0.18), residues: 780 loop : -0.39 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 393 TYR 0.010 0.001 TYR B 235 PHE 0.021 0.002 PHE F 301 TRP 0.025 0.002 TRP A 92 HIS 0.003 0.000 HIS C 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (23644) covalent geometry : angle 0.45413 / 0.25 (31958) hydrogen bonds : bond 0.03039 / 2.07 ( 1092) hydrogen bonds : angle 4.13938 / 2.92 ( 3060) Misc. bond : bond 0.00164 / 0.09 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 0.941 Fit side-chains REVERT: A 77 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7384 (pt0) REVERT: A 88 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7787 (tpp80) REVERT: A 232 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.7723 (mmtt) REVERT: A 336 GLU cc_start: 0.8201 (tp30) cc_final: 0.7820 (tt0) REVERT: A 357 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7250 (pt0) REVERT: A 362 ILE cc_start: 0.8520 (mm) cc_final: 0.8287 (mp) REVERT: A 390 ASN cc_start: 0.8503 (m-40) cc_final: 0.8259 (m110) REVERT: A 404 LYS cc_start: 0.8030 (mttt) cc_final: 0.7684 (mttm) REVERT: A 461 SER cc_start: 0.9210 (t) cc_final: 0.8944 (p) REVERT: B 128 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 150 VAL cc_start: 0.8090 (m) cc_final: 0.7800 (p) REVERT: B 247 PHE cc_start: 0.7692 (m-80) cc_final: 0.7124 (t80) REVERT: B 357 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: B 362 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8454 (mp) REVERT: B 461 SER cc_start: 0.9364 (t) cc_final: 0.9128 (p) REVERT: B 471 MET cc_start: 0.8425 (mpp) cc_final: 0.8010 (mpp) REVERT: B 480 LYS cc_start: 0.8316 (mttp) cc_final: 0.7952 (mttm) REVERT: B 487 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7576 (mt-10) REVERT: C 106 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8457 (tt) REVERT: C 128 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7612 (mm-30) REVERT: C 150 VAL cc_start: 0.7762 (m) cc_final: 0.7401 (p) REVERT: C 357 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: C 393 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6998 (mtm110) REVERT: C 487 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7324 (mt-10) REVERT: D 77 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7414 (pt0) REVERT: D 162 ARG cc_start: 0.7551 (ttp-170) cc_final: 0.7347 (ttp80) REVERT: D 232 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.7707 (mmtt) REVERT: D 257 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7274 (mmt180) REVERT: D 336 GLU cc_start: 0.8042 (tt0) cc_final: 0.7515 (tt0) REVERT: D 357 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: D 390 ASN cc_start: 0.8509 (m-40) cc_final: 0.8279 (m110) REVERT: D 461 SER cc_start: 0.9222 (t) cc_final: 0.8964 (p) REVERT: E 247 PHE cc_start: 0.7682 (m-80) cc_final: 0.7121 (t80) REVERT: E 362 ILE cc_start: 0.8841 (mt) cc_final: 0.8535 (mt) REVERT: E 488 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7637 (mtm-85) REVERT: F 54 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8578 (tt) REVERT: F 106 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8475 (tt) REVERT: F 124 SER cc_start: 0.7613 (m) cc_final: 0.7055 (t) REVERT: F 128 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7552 (mm-30) REVERT: F 147 VAL cc_start: 0.8781 (m) cc_final: 0.8555 (m) REVERT: F 150 VAL cc_start: 0.7790 (m) cc_final: 0.7426 (p) REVERT: F 357 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: F 393 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.6996 (mtm110) REVERT: F 471 MET cc_start: 0.8417 (mpp) cc_final: 0.8156 (pmm) REVERT: F 487 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7289 (mt-10) outliers start: 48 outliers final: 28 residues processed: 325 average time/residue: 0.6826 time to fit residues: 249.0385 Evaluate side-chains 322 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 173 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 219 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 368 ASN E 361 GLN F 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108449 restraints weight = 29096.436| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.04 r_work: 0.3160 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 23656 Z= 0.252 Angle : 0.545 6.084 31958 Z= 0.291 Chirality : 0.046 0.236 3558 Planarity : 0.004 0.049 4090 Dihedral : 5.926 81.052 3240 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.21 % Allowed : 16.56 % Favored : 81.23 % 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: 0.53 (0.15), residues: 2898 helix: 1.66 (0.16), residues: 1080 sheet: -0.24 (0.18), residues: 792 loop : -0.45 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 393 TYR 0.013 0.002 TYR C 235 PHE 0.027 0.002 PHE F 301 TRP 0.026 0.003 TRP E 92 HIS 0.004 0.001 HIS E 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.25 (23644) covalent geometry : angle 0.54502 / 0.29 (31958) hydrogen bonds : bond 0.03749 / 2.56 ( 1092) hydrogen bonds : angle 4.36028 / 3.08 ( 3060) Misc. bond : bond 0.00284 / 0.16 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6980.70 seconds wall clock time: 119 minutes 33.84 seconds (7173.84 seconds total)