Starting phenix.real_space_refine on Thu Mar 5 14:09:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s66_24851/03_2026/7s66_24851.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s66_24851/03_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_24851/03_2026/7s66_24851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s66_24851/03_2026/7s66_24851.map" model { file = "/net/cci-nas-00/data/ceres_data/7s66_24851/03_2026/7s66_24851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s66_24851/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 5.95, per 1000 atoms: 0.26 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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.77 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: 4.41 Time building geometry restraints manager: 2.47 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 - 17.95: 13664 17.95 - 35.90: 514 35.90 - 53.85: 150 53.85 - 71.80: 54 71.80 - 89.74: 24 Dihedral angle restraints: 14406 sinusoidal: 6090 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 14403 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: 0.06 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.490 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 12.056 89.744 9066 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 covalent geometry : bond 0.01289 (23644) covalent geometry : angle 1.34395 (31958) hydrogen bonds : bond 0.16213 ( 1092) hydrogen bonds : angle 6.91616 ( 3060) Misc. bond : bond 0.76545 ( 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 : 0.769 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: 0.8321 time to fit residues: 564.8715 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 : 1.073 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111170 restraints weight = 27837.107| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.15 r_work: 0.3239 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23656 Z= 0.131 Angle : 0.507 5.692 31958 Z= 0.283 Chirality : 0.043 0.135 3558 Planarity : 0.004 0.030 4090 Dihedral : 10.727 87.813 3612 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.82 % Allowed : 10.67 % Favored : 86.51 % 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: 1.00 (0.15), residues: 2898 helix: 1.39 (0.16), residues: 1044 sheet: 0.40 (0.19), residues: 780 loop : 0.32 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 340 TYR 0.015 0.002 TYR E 154 PHE 0.020 0.002 PHE D 301 TRP 0.031 0.003 TRP C 92 HIS 0.007 0.001 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00290 (23644) covalent geometry : angle 0.50656 (31958) hydrogen bonds : bond 0.03989 ( 1092) hydrogen bonds : angle 4.78613 ( 3060) Misc. bond : bond 0.00333 ( 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 419 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 350 time to evaluate : 0.598 Fit side-chains REVERT: A 336 GLU cc_start: 0.8000 (tp30) cc_final: 0.7753 (tt0) REVERT: A 357 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: A 393 ARG cc_start: 0.7259 (mtm110) cc_final: 0.6907 (mtm110) REVERT: A 404 LYS cc_start: 0.7872 (mttt) cc_final: 0.7530 (mttm) REVERT: A 426 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7780 (t) REVERT: B 128 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 357 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: B 471 MET cc_start: 0.8349 (mpp) cc_final: 0.8010 (mpp) REVERT: B 480 LYS cc_start: 0.7977 (mttp) cc_final: 0.7638 (mttp) REVERT: B 487 GLU cc_start: 0.7661 (mt-10) cc_final: 0.6967 (mt-10) REVERT: B 488 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7363 (mtm110) REVERT: C 81 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7805 (mp10) REVERT: C 393 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6760 (mtm110) REVERT: C 426 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8048 (t) REVERT: C 448 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7112 (mt-10) REVERT: C 487 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6881 (mt-10) REVERT: D 336 GLU cc_start: 0.7825 (tt0) cc_final: 0.7443 (tt0) REVERT: D 357 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: D 393 ARG cc_start: 0.7232 (mtm110) cc_final: 0.6864 (mtm110) REVERT: D 426 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7809 (t) REVERT: D 471 MET cc_start: 0.8443 (mpp) cc_final: 0.8204 (mpp) REVERT: E 257 ARG cc_start: 0.7135 (mmt180) cc_final: 0.6894 (mtm-85) REVERT: E 362 ILE cc_start: 0.8549 (mt) cc_final: 0.8116 (mp) REVERT: E 480 LYS cc_start: 0.7980 (mttp) cc_final: 0.7677 (mttp) REVERT: E 487 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6959 (mt-10) REVERT: E 488 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7331 (mtm110) REVERT: F 81 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: F 253 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7327 (mmp80) REVERT: F 333 MET cc_start: 0.8249 (mtp) cc_final: 0.7939 (mtp) REVERT: F 393 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6766 (mtm110) REVERT: F 407 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7534 (mm-30) REVERT: F 448 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7133 (mt-10) REVERT: F 487 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6935 (mt-10) outliers start: 69 outliers final: 15 residues processed: 407 average time/residue: 0.7223 time to fit residues: 331.1895 Evaluate side-chains 318 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 228 THR 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 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: 6.9990 chunk 187 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 233 optimal weight: 0.0370 chunk 169 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3662 r_free = 0.3662 target = 0.134788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110438 restraints weight = 28717.212| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.04 r_work: 0.3186 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 23656 Z= 0.269 Angle : 0.592 7.119 31958 Z= 0.320 Chirality : 0.047 0.213 3558 Planarity : 0.004 0.032 4090 Dihedral : 11.056 77.576 3612 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.80 % Allowed : 10.96 % Favored : 85.24 % 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: 1.27 (0.16), residues: 1080 sheet: 0.03 (0.18), residues: 756 loop : -0.25 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 326 TYR 0.017 0.003 TYR F 350 PHE 0.030 0.003 PHE C 301 TRP 0.035 0.004 TRP E 92 HIS 0.010 0.002 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00653 (23644) covalent geometry : angle 0.59169 (31958) hydrogen bonds : bond 0.04472 ( 1092) hydrogen bonds : angle 4.74625 ( 3060) Misc. bond : bond 0.00280 ( 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 419 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 326 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7446 (pt0) REVERT: A 162 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7466 (ttp80) REVERT: A 235 TYR cc_start: 0.9163 (m-80) cc_final: 0.8876 (m-80) REVERT: A 269 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7172 (tmt170) REVERT: A 336 GLU cc_start: 0.8142 (tp30) cc_final: 0.7833 (tt0) REVERT: A 362 ILE cc_start: 0.8722 (mm) cc_final: 0.8433 (mp) REVERT: A 404 LYS cc_start: 0.7977 (mttt) cc_final: 0.7650 (mttm) REVERT: A 488 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7381 (mtm-85) REVERT: B 106 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8710 (tt) REVERT: B 128 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7657 (mm-30) REVERT: B 247 PHE cc_start: 0.7608 (m-80) cc_final: 0.7052 (t80) REVERT: B 357 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: B 362 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 471 MET cc_start: 0.8471 (mpp) cc_final: 0.8115 (mpp) REVERT: B 480 LYS cc_start: 0.8501 (mttp) cc_final: 0.8153 (mttm) REVERT: B 487 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7511 (mt-10) REVERT: B 488 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7801 (mtm110) REVERT: C 128 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7520 (mm-30) REVERT: C 281 ASP cc_start: 0.8278 (m-30) cc_final: 0.8029 (m-30) REVERT: C 357 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: C 393 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7164 (mtm110) REVERT: C 431 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: C 487 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7335 (mt-10) REVERT: D 77 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7450 (pt0) REVERT: D 162 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7490 (ttp80) REVERT: D 235 TYR cc_start: 0.9170 (m-80) cc_final: 0.8812 (m-80) REVERT: D 269 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7194 (tmt170) REVERT: D 336 GLU cc_start: 0.8025 (tt0) cc_final: 0.7586 (tt0) REVERT: D 362 ILE cc_start: 0.8752 (mm) cc_final: 0.8468 (mp) REVERT: D 488 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7368 (mtm-85) REVERT: E 128 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7601 (mm-30) REVERT: E 247 PHE cc_start: 0.7595 (m-80) cc_final: 0.7031 (t80) REVERT: E 257 ARG cc_start: 0.7352 (mmt180) cc_final: 0.7109 (mtm-85) REVERT: E 362 ILE cc_start: 0.8861 (mt) cc_final: 0.8433 (mp) REVERT: E 471 MET cc_start: 0.8481 (mpp) cc_final: 0.7901 (mpt) REVERT: E 480 LYS cc_start: 0.8480 (mttp) cc_final: 0.8269 (mttp) REVERT: E 487 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7444 (mt-10) REVERT: E 488 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7788 (mtm110) REVERT: F 124 SER cc_start: 0.7589 (m) cc_final: 0.7096 (t) REVERT: F 128 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7492 (mm-30) REVERT: F 357 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: F 393 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7166 (mtm110) REVERT: F 471 MET cc_start: 0.8367 (mpp) cc_final: 0.8163 (mpp) REVERT: F 487 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7327 (mt-10) outliers start: 93 outliers final: 44 residues processed: 404 average time/residue: 0.7721 time to fit residues: 348.0242 Evaluate side-chains 328 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 269 ARG 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 106 LEU 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 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 64 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 269 ARG 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 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 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: 0.9990 chunk 216 optimal weight: 0.0170 chunk 50 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 285 optimal weight: 7.9990 chunk 273 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113213 restraints weight = 28790.651| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.05 r_work: 0.3244 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3414 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= 0.096 Angle : 0.430 5.444 31958 Z= 0.239 Chirality : 0.041 0.140 3558 Planarity : 0.003 0.041 4090 Dihedral : 10.222 88.364 3612 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.90 % Allowed : 13.49 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2898 helix: 1.89 (0.16), residues: 1044 sheet: 0.08 (0.19), residues: 756 loop : -0.08 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 340 TYR 0.011 0.001 TYR A 154 PHE 0.018 0.001 PHE F 301 TRP 0.026 0.002 TRP A 92 HIS 0.002 0.000 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00201 (23644) covalent geometry : angle 0.43011 (31958) hydrogen bonds : bond 0.03068 ( 1092) hydrogen bonds : angle 4.35146 ( 3060) Misc. bond : bond 0.00066 ( 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 395 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 324 time to evaluate : 0.846 Fit side-chains REVERT: A 77 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7395 (pt0) REVERT: A 162 ARG cc_start: 0.7635 (ttp-170) cc_final: 0.7376 (ttp80) REVERT: A 269 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7416 (tmt170) REVERT: A 336 GLU cc_start: 0.8147 (tp30) cc_final: 0.7828 (tt0) REVERT: A 357 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: A 358 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: A 404 LYS cc_start: 0.8039 (mttt) cc_final: 0.7729 (mttm) REVERT: A 461 SER cc_start: 0.9173 (t) cc_final: 0.8907 (p) REVERT: A 480 LYS cc_start: 0.8144 (mttm) cc_final: 0.7799 (mttp) REVERT: A 488 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7262 (mtm-85) REVERT: B 128 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 150 VAL cc_start: 0.7997 (m) cc_final: 0.7768 (p) REVERT: B 247 PHE cc_start: 0.7523 (m-80) cc_final: 0.6963 (t80) REVERT: B 357 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: B 362 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8677 (mp) REVERT: B 471 MET cc_start: 0.8403 (mpp) cc_final: 0.8029 (mpp) REVERT: B 480 LYS cc_start: 0.8422 (mttp) cc_final: 0.8119 (mttp) REVERT: B 487 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7421 (mt-10) REVERT: C 81 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: C 128 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 150 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7695 (p) REVERT: C 281 ASP cc_start: 0.8058 (m-30) cc_final: 0.7827 (m-30) REVERT: C 357 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: C 393 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7066 (mtm110) REVERT: C 431 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: C 487 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7162 (mt-10) REVERT: D 77 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7408 (pt0) REVERT: D 162 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7386 (ttp80) REVERT: D 269 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7502 (tmt170) REVERT: D 310 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: D 336 GLU cc_start: 0.8079 (tt0) cc_final: 0.7584 (tt0) REVERT: D 357 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: D 461 SER cc_start: 0.9179 (t) cc_final: 0.8917 (p) REVERT: D 488 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7271 (mtm-85) REVERT: E 150 VAL cc_start: 0.7989 (m) cc_final: 0.7760 (p) REVERT: E 247 PHE cc_start: 0.7508 (m-80) cc_final: 0.6960 (t80) REVERT: E 257 ARG cc_start: 0.7258 (mmt180) cc_final: 0.7008 (mtm-85) REVERT: E 362 ILE cc_start: 0.8893 (mt) cc_final: 0.8495 (mp) REVERT: E 480 LYS cc_start: 0.8469 (mttp) cc_final: 0.8257 (mttp) REVERT: E 487 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7403 (mt-10) REVERT: F 81 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: F 124 SER cc_start: 0.7585 (m) cc_final: 0.7099 (t) REVERT: F 128 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7487 (mm-30) REVERT: F 357 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: F 393 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7035 (mtm110) REVERT: F 471 MET cc_start: 0.8356 (mpp) cc_final: 0.8135 (mpp) REVERT: F 480 LYS cc_start: 0.8449 (mttp) cc_final: 0.8090 (mttp) REVERT: F 487 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7162 (mt-10) outliers start: 71 outliers final: 26 residues processed: 383 average time/residue: 0.7801 time to fit residues: 334.7264 Evaluate side-chains 330 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 288 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 358 ASP 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 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 81 GLN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 217 ARG 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 D residue 65 ILE 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 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 64 ILE 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 379 SER 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: 0.2980 chunk 27 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110853 restraints weight = 28706.558| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.03 r_work: 0.3205 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23656 Z= 0.164 Angle : 0.474 5.737 31958 Z= 0.259 Chirality : 0.043 0.151 3558 Planarity : 0.003 0.046 4090 Dihedral : 10.408 89.639 3612 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.31 % Allowed : 13.98 % Favored : 82.71 % 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: 0.92 (0.16), residues: 2898 helix: 1.95 (0.16), residues: 1038 sheet: 0.05 (0.18), residues: 756 loop : -0.17 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 340 TYR 0.015 0.002 TYR B 235 PHE 0.024 0.002 PHE C 301 TRP 0.026 0.002 TRP A 92 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00392 (23644) covalent geometry : angle 0.47389 (31958) hydrogen bonds : bond 0.03405 ( 1092) hydrogen bonds : angle 4.31990 ( 3060) Misc. bond : bond 0.00279 ( 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 378 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 297 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8071 (ptm) cc_final: 0.7802 (ptm) REVERT: A 77 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7412 (pt0) REVERT: A 88 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7789 (mmt-90) REVERT: A 162 ARG cc_start: 0.7592 (ttp-170) cc_final: 0.7361 (ttp80) REVERT: A 269 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7501 (tmt170) REVERT: A 336 GLU cc_start: 0.8169 (tp30) cc_final: 0.7852 (tt0) REVERT: A 404 LYS cc_start: 0.8046 (mttt) cc_final: 0.7710 (mttm) REVERT: A 431 GLU cc_start: 0.8325 (pt0) cc_final: 0.8059 (mp0) REVERT: A 461 SER cc_start: 0.9241 (t) cc_final: 0.8968 (p) REVERT: B 128 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7669 (mm-30) REVERT: B 150 VAL cc_start: 0.8080 (OUTLIER) cc_final: 0.7831 (p) REVERT: B 247 PHE cc_start: 0.7662 (m-80) cc_final: 0.7054 (t80) REVERT: B 357 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: B 362 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8646 (mp) REVERT: B 471 MET cc_start: 0.8436 (mpp) cc_final: 0.8033 (mpp) REVERT: B 480 LYS cc_start: 0.8390 (mttp) cc_final: 0.8029 (mttp) REVERT: C 106 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8495 (tt) REVERT: C 128 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7615 (mm-30) REVERT: C 357 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: C 393 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7015 (mtm110) REVERT: C 431 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: C 487 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7196 (mt-10) REVERT: D 21 MET cc_start: 0.7862 (ptm) cc_final: 0.7657 (ptm) REVERT: D 77 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7431 (pt0) REVERT: D 88 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7796 (mmt-90) REVERT: D 162 ARG cc_start: 0.7592 (ttp-170) cc_final: 0.7374 (ttp80) REVERT: D 269 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7504 (tmt170) REVERT: D 310 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: D 336 GLU cc_start: 0.8079 (tt0) cc_final: 0.7544 (tt0) REVERT: D 431 GLU cc_start: 0.8512 (pt0) cc_final: 0.8284 (mp0) REVERT: D 461 SER cc_start: 0.9240 (t) cc_final: 0.8967 (p) REVERT: D 480 LYS cc_start: 0.8200 (mttp) cc_final: 0.7973 (mttp) REVERT: E 150 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7810 (p) REVERT: E 247 PHE cc_start: 0.7640 (m-80) cc_final: 0.7044 (t80) REVERT: E 257 ARG cc_start: 0.7221 (mmt180) cc_final: 0.6937 (mtm-85) REVERT: E 362 ILE cc_start: 0.8867 (mt) cc_final: 0.8535 (mp) REVERT: E 480 LYS cc_start: 0.8279 (mttp) cc_final: 0.8061 (mttp) REVERT: F 106 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8503 (tt) REVERT: F 124 SER cc_start: 0.7593 (m) cc_final: 0.7110 (t) REVERT: F 128 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7450 (mm-30) REVERT: F 150 VAL cc_start: 0.7873 (m) cc_final: 0.7608 (p) REVERT: F 357 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: F 393 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6993 (mtm110) REVERT: F 431 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: F 471 MET cc_start: 0.8365 (mpp) cc_final: 0.8140 (mpp) REVERT: F 480 LYS cc_start: 0.8446 (mttp) cc_final: 0.8100 (mttp) REVERT: F 487 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7198 (mt-10) outliers start: 81 outliers final: 43 residues processed: 363 average time/residue: 0.8056 time to fit residues: 326.5461 Evaluate side-chains 332 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 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 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 471 MET Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 150 VAL 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 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 217 ARG 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 D residue 57 ILE Chi-restraints excluded: chain D residue 64 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 471 MET Chi-restraints excluded: chain E residue 150 VAL 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 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 379 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: 10.0000 chunk 80 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109748 restraints weight = 29033.820| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.03 r_work: 0.3187 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 23656 Z= 0.197 Angle : 0.506 13.247 31958 Z= 0.273 Chirality : 0.044 0.155 3558 Planarity : 0.004 0.053 4090 Dihedral : 10.451 89.310 3612 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.19 % Allowed : 14.10 % Favored : 82.71 % 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: 0.65 (0.15), residues: 2898 helix: 1.67 (0.16), residues: 1074 sheet: 0.01 (0.19), residues: 756 loop : -0.42 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 140 TYR 0.016 0.002 TYR B 235 PHE 0.025 0.002 PHE F 301 TRP 0.026 0.003 TRP E 92 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00479 (23644) covalent geometry : angle 0.50633 (31958) hydrogen bonds : bond 0.03477 ( 1092) hydrogen bonds : angle 4.33251 ( 3060) Misc. bond : bond 0.00253 ( 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 359 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 281 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8180 (ptm) cc_final: 0.7867 (ptm) REVERT: A 77 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7495 (pt0) REVERT: A 88 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7825 (mmt-90) REVERT: A 162 ARG cc_start: 0.7612 (ttp-170) cc_final: 0.7383 (ttp80) REVERT: A 269 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7504 (tmt170) REVERT: A 336 GLU cc_start: 0.8224 (tp30) cc_final: 0.7856 (tt0) REVERT: A 404 LYS cc_start: 0.8078 (mttt) cc_final: 0.7744 (mttm) REVERT: A 461 SER cc_start: 0.9256 (t) cc_final: 0.8989 (p) REVERT: B 128 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7714 (mm-30) REVERT: B 150 VAL cc_start: 0.8015 (m) cc_final: 0.7739 (p) REVERT: B 247 PHE cc_start: 0.7645 (m-80) cc_final: 0.7076 (t80) REVERT: B 357 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: B 362 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8685 (mp) REVERT: B 471 MET cc_start: 0.8440 (mpp) cc_final: 0.8043 (mpp) REVERT: B 480 LYS cc_start: 0.8422 (mttp) cc_final: 0.8046 (mttm) REVERT: C 106 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8407 (tt) REVERT: C 128 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 150 VAL cc_start: 0.7826 (m) cc_final: 0.7526 (p) REVERT: C 357 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: C 393 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7029 (mtm110) REVERT: C 431 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: C 487 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7247 (mt-10) REVERT: D 21 MET cc_start: 0.8061 (ptm) cc_final: 0.7787 (ptm) REVERT: D 77 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7412 (pt0) REVERT: D 88 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7825 (mmt-90) REVERT: D 162 ARG cc_start: 0.7621 (ttp-170) cc_final: 0.7403 (ttp80) REVERT: D 269 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7508 (tmt170) REVERT: D 310 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: D 336 GLU cc_start: 0.8051 (tt0) cc_final: 0.7550 (tt0) REVERT: D 390 ASN cc_start: 0.8504 (m-40) cc_final: 0.8250 (m110) REVERT: D 461 SER cc_start: 0.9258 (t) cc_final: 0.8986 (p) REVERT: E 150 VAL cc_start: 0.7959 (m) cc_final: 0.7658 (p) REVERT: E 247 PHE cc_start: 0.7639 (m-80) cc_final: 0.7066 (t80) REVERT: E 257 ARG cc_start: 0.7215 (mmt180) cc_final: 0.6950 (mtm-85) REVERT: E 362 ILE cc_start: 0.8888 (mt) cc_final: 0.8511 (mp) REVERT: E 471 MET cc_start: 0.8334 (mpp) cc_final: 0.7779 (mpt) REVERT: F 106 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8373 (tt) REVERT: F 128 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7537 (mm-30) REVERT: F 150 VAL cc_start: 0.7755 (m) cc_final: 0.7482 (p) REVERT: F 357 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: F 393 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7001 (mtm110) REVERT: F 431 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: F 471 MET cc_start: 0.8425 (mpp) cc_final: 0.8214 (mpp) REVERT: F 480 LYS cc_start: 0.8420 (mttp) cc_final: 0.8051 (mttp) REVERT: F 487 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7270 (mt-10) outliers start: 78 outliers final: 46 residues processed: 349 average time/residue: 0.7832 time to fit residues: 304.3521 Evaluate side-chains 327 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 268 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 269 ARG 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 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 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 439 LEU 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 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 471 MET 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 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 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 379 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111716 restraints weight = 28995.962| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.03 r_work: 0.3219 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23656 Z= 0.115 Angle : 0.440 7.855 31958 Z= 0.241 Chirality : 0.041 0.155 3558 Planarity : 0.003 0.038 4090 Dihedral : 10.035 85.125 3612 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.70 % Allowed : 15.21 % Favored : 82.09 % 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 (0.15), residues: 2898 helix: 1.83 (0.16), residues: 1074 sheet: 0.10 (0.19), residues: 756 loop : -0.39 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 140 TYR 0.012 0.001 TYR B 235 PHE 0.018 0.001 PHE F 301 TRP 0.024 0.002 TRP A 92 HIS 0.002 0.000 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00265 (23644) covalent geometry : angle 0.44013 (31958) hydrogen bonds : bond 0.02970 ( 1092) hydrogen bonds : angle 4.20014 ( 3060) Misc. bond : bond 0.00108 ( 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 368 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 302 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8229 (ptm) cc_final: 0.7984 (ptm) REVERT: A 77 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7388 (pt0) REVERT: A 88 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7677 (tpp80) REVERT: A 162 ARG cc_start: 0.7590 (ttp-170) cc_final: 0.7359 (ttp80) REVERT: A 232 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.7778 (mmtt) REVERT: A 336 GLU cc_start: 0.8104 (tp30) cc_final: 0.7812 (tt0) REVERT: A 404 LYS cc_start: 0.8079 (mttt) cc_final: 0.7750 (mttm) REVERT: A 461 SER cc_start: 0.9207 (t) cc_final: 0.8966 (p) REVERT: B 128 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7673 (mm-30) REVERT: B 150 VAL cc_start: 0.8023 (m) cc_final: 0.7738 (p) REVERT: B 247 PHE cc_start: 0.7641 (m-80) cc_final: 0.7098 (t80) REVERT: B 357 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 362 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8717 (mp) REVERT: B 471 MET cc_start: 0.8414 (mpp) cc_final: 0.8073 (mpp) REVERT: B 480 LYS cc_start: 0.8455 (mttp) cc_final: 0.8120 (mttp) REVERT: B 488 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7238 (mtm-85) REVERT: C 106 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8507 (tt) REVERT: C 128 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7579 (mm-30) REVERT: C 150 VAL cc_start: 0.7758 (m) cc_final: 0.7434 (p) REVERT: C 357 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: C 393 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7007 (mtm110) REVERT: C 487 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7231 (mt-10) REVERT: D 21 MET cc_start: 0.8081 (ptm) cc_final: 0.7846 (ptm) REVERT: D 77 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7393 (pt0) REVERT: D 88 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7702 (tpp80) REVERT: D 162 ARG cc_start: 0.7622 (ttp-170) cc_final: 0.7409 (ttp80) REVERT: D 232 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.7761 (mmtt) REVERT: D 336 GLU cc_start: 0.8081 (tt0) cc_final: 0.7589 (tt0) REVERT: D 390 ASN cc_start: 0.8482 (m-40) cc_final: 0.8229 (m110) REVERT: D 461 SER cc_start: 0.9212 (t) cc_final: 0.8974 (p) REVERT: E 150 VAL cc_start: 0.8037 (m) cc_final: 0.7743 (p) REVERT: E 247 PHE cc_start: 0.7641 (m-80) cc_final: 0.7093 (t80) REVERT: E 257 ARG cc_start: 0.7189 (mmt180) cc_final: 0.6934 (mtm-85) REVERT: E 362 ILE cc_start: 0.8873 (mt) cc_final: 0.8557 (mp) REVERT: E 461 SER cc_start: 0.9348 (t) cc_final: 0.9101 (p) REVERT: E 471 MET cc_start: 0.8362 (mpp) cc_final: 0.7972 (mpt) REVERT: E 488 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7230 (mtm-85) REVERT: F 106 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8513 (tt) REVERT: F 124 SER cc_start: 0.7633 (m) cc_final: 0.7102 (t) REVERT: F 128 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7539 (mm-30) REVERT: F 150 VAL cc_start: 0.7861 (m) cc_final: 0.7555 (p) REVERT: F 357 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: F 393 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7027 (mtm110) REVERT: F 431 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: F 480 LYS cc_start: 0.8360 (mttp) cc_final: 0.8058 (mttp) REVERT: F 487 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7249 (mt-10) outliers start: 66 outliers final: 35 residues processed: 360 average time/residue: 0.7891 time to fit residues: 316.8129 Evaluate side-chains 328 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS 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 471 MET Chi-restraints excluded: chain A residue 480 LYS 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 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 232 LYS 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 407 GLU 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 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 379 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 281 optimal weight: 7.9990 chunk 278 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 250 optimal weight: 40.0000 chunk 123 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 overall best weight: 3.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108448 restraints weight = 29055.195| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.03 r_work: 0.3168 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3874 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= 0.237 Angle : 0.526 5.914 31958 Z= 0.283 Chirality : 0.045 0.178 3558 Planarity : 0.004 0.043 4090 Dihedral : 10.362 85.843 3612 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.98 % Allowed : 14.84 % Favored : 82.17 % 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: 0.57 (0.15), residues: 2898 helix: 1.67 (0.16), residues: 1074 sheet: -0.04 (0.18), residues: 756 loop : -0.54 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 140 TYR 0.020 0.002 TYR B 235 PHE 0.026 0.002 PHE F 301 TRP 0.025 0.003 TRP E 92 HIS 0.004 0.001 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00582 (23644) covalent geometry : angle 0.52575 (31958) hydrogen bonds : bond 0.03658 ( 1092) hydrogen bonds : angle 4.33396 ( 3060) Misc. bond : bond 0.00245 ( 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 357 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 284 time to evaluate : 0.886 Fit side-chains REVERT: A 21 MET cc_start: 0.8292 (ptm) cc_final: 0.8016 (ptm) REVERT: A 77 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7407 (pt0) REVERT: A 88 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7779 (tpp80) REVERT: A 162 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7429 (ttp80) REVERT: A 336 GLU cc_start: 0.8192 (tp30) cc_final: 0.7850 (tt0) REVERT: A 362 ILE cc_start: 0.8601 (mm) cc_final: 0.8343 (mp) REVERT: A 390 ASN cc_start: 0.8539 (m-40) cc_final: 0.8312 (m110) REVERT: A 404 LYS cc_start: 0.8076 (mttt) cc_final: 0.7731 (mttm) REVERT: A 461 SER cc_start: 0.9266 (t) cc_final: 0.8994 (p) REVERT: B 128 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 247 PHE cc_start: 0.7708 (m-80) cc_final: 0.7109 (t80) REVERT: B 357 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 362 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 449 MET cc_start: 0.9039 (mmm) cc_final: 0.8806 (mtp) REVERT: B 471 MET cc_start: 0.8456 (mpp) cc_final: 0.8117 (mpp) REVERT: B 480 LYS cc_start: 0.8357 (mttp) cc_final: 0.7959 (mttm) REVERT: B 487 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7603 (mt-10) REVERT: C 106 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8379 (tt) REVERT: C 128 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7565 (mm-30) REVERT: C 150 VAL cc_start: 0.7853 (m) cc_final: 0.7539 (p) REVERT: C 357 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: C 393 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7027 (mtm110) REVERT: C 487 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7312 (mt-10) REVERT: D 21 MET cc_start: 0.8267 (ptm) cc_final: 0.7933 (ptm) REVERT: D 77 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7421 (pt0) REVERT: D 88 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7795 (tpp80) REVERT: D 162 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7424 (ttp80) REVERT: D 232 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.7765 (mmtt) REVERT: D 336 GLU cc_start: 0.8089 (tt0) cc_final: 0.7575 (tt0) REVERT: D 390 ASN cc_start: 0.8532 (m-40) cc_final: 0.8322 (m110) REVERT: D 461 SER cc_start: 0.9268 (t) cc_final: 0.9000 (p) REVERT: E 247 PHE cc_start: 0.7713 (m-80) cc_final: 0.7089 (t80) REVERT: E 257 ARG cc_start: 0.7192 (mmt180) cc_final: 0.6925 (mtm-85) REVERT: E 362 ILE cc_start: 0.8855 (mt) cc_final: 0.8494 (mp) REVERT: E 487 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7552 (mt-10) REVERT: F 54 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8638 (tt) REVERT: F 106 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8397 (tt) REVERT: F 128 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7522 (mm-30) REVERT: F 150 VAL cc_start: 0.7846 (m) cc_final: 0.7552 (p) REVERT: F 357 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7441 (pt0) REVERT: F 393 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7013 (mtm110) REVERT: F 431 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: F 487 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7326 (mt-10) outliers start: 73 outliers final: 36 residues processed: 339 average time/residue: 0.7606 time to fit residues: 287.8231 Evaluate side-chains 318 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE 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 A residue 493 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 365 SER Chi-restraints excluded: chain B residue 379 SER 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 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 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 493 SER 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 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 379 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 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: 4.9990 chunk 134 optimal weight: 0.7980 chunk 194 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110268 restraints weight = 29092.169| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.01 r_work: 0.3198 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23656 Z= 0.149 Angle : 0.464 5.611 31958 Z= 0.253 Chirality : 0.042 0.146 3558 Planarity : 0.003 0.035 4090 Dihedral : 9.885 87.307 3612 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.25 % Allowed : 15.90 % Favored : 81.85 % 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: 0.67 (0.15), residues: 2898 helix: 1.79 (0.16), residues: 1074 sheet: -0.01 (0.19), residues: 756 loop : -0.51 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 393 TYR 0.015 0.001 TYR B 235 PHE 0.020 0.002 PHE F 301 TRP 0.027 0.002 TRP A 92 HIS 0.002 0.000 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00355 (23644) covalent geometry : angle 0.46374 (31958) hydrogen bonds : bond 0.03139 ( 1092) hydrogen bonds : angle 4.22777 ( 3060) Misc. bond : bond 0.00158 ( 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 340 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 285 time to evaluate : 0.892 Fit side-chains REVERT: A 21 MET cc_start: 0.8318 (ptm) cc_final: 0.8069 (ptm) REVERT: A 77 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7428 (pt0) REVERT: A 162 ARG cc_start: 0.7629 (ttp-170) cc_final: 0.7422 (ttp80) REVERT: A 232 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.7739 (mmtt) REVERT: A 336 GLU cc_start: 0.8190 (tp30) cc_final: 0.7845 (tt0) REVERT: A 357 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: A 390 ASN cc_start: 0.8511 (m-40) cc_final: 0.8272 (m110) REVERT: A 404 LYS cc_start: 0.8086 (mttt) cc_final: 0.7751 (mttm) REVERT: A 461 SER cc_start: 0.9210 (t) cc_final: 0.8980 (p) REVERT: B 128 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 247 PHE cc_start: 0.7684 (m-80) cc_final: 0.7137 (t80) REVERT: B 357 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: B 362 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 449 MET cc_start: 0.8965 (mmm) cc_final: 0.8666 (mtt) REVERT: B 471 MET cc_start: 0.8413 (mpp) cc_final: 0.8077 (mpp) REVERT: B 480 LYS cc_start: 0.8391 (mttp) cc_final: 0.8044 (mttm) REVERT: B 488 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7298 (mtm-85) REVERT: C 106 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8396 (tt) REVERT: C 128 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7557 (mm-30) REVERT: C 147 VAL cc_start: 0.8776 (m) cc_final: 0.8526 (m) REVERT: C 150 VAL cc_start: 0.7785 (m) cc_final: 0.7461 (p) REVERT: C 357 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: C 393 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7015 (mtm110) REVERT: C 487 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7299 (mt-10) REVERT: D 21 MET cc_start: 0.8316 (ptm) cc_final: 0.8008 (ptm) REVERT: D 77 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7455 (pt0) REVERT: D 162 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7416 (ttp80) REVERT: D 232 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.7729 (mmtt) REVERT: D 336 GLU cc_start: 0.8066 (tt0) cc_final: 0.7552 (tt0) REVERT: D 357 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: D 390 ASN cc_start: 0.8512 (m-40) cc_final: 0.8275 (m110) REVERT: D 461 SER cc_start: 0.9208 (t) cc_final: 0.8989 (p) REVERT: E 247 PHE cc_start: 0.7670 (m-80) cc_final: 0.7132 (t80) REVERT: E 257 ARG cc_start: 0.7195 (mmt180) cc_final: 0.6944 (mtm-85) REVERT: E 362 ILE cc_start: 0.8852 (mt) cc_final: 0.8542 (mt) REVERT: E 461 SER cc_start: 0.9371 (t) cc_final: 0.9122 (p) REVERT: E 488 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7266 (mtm-85) REVERT: F 106 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8400 (tt) REVERT: F 128 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7503 (mm-30) REVERT: F 150 VAL cc_start: 0.7808 (m) cc_final: 0.7489 (p) REVERT: F 357 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: F 393 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6994 (mtm110) REVERT: F 431 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: F 487 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7340 (mt-10) outliers start: 55 outliers final: 32 residues processed: 334 average time/residue: 0.7856 time to fit residues: 293.4134 Evaluate side-chains 320 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS 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 A residue 493 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 365 SER Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 493 SER 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 379 SER 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 232 LYS 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 493 SER 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 493 SER 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 379 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 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: 0.0030 chunk 235 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 279 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 154 optimal weight: 30.0000 chunk 166 optimal weight: 2.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110388 restraints weight = 29015.249| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.04 r_work: 0.3205 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3992 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= 0.134 Angle : 0.452 5.644 31958 Z= 0.247 Chirality : 0.042 0.144 3558 Planarity : 0.003 0.036 4090 Dihedral : 9.647 89.154 3612 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.04 % Allowed : 16.27 % Favored : 81.68 % 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: 0.74 (0.15), residues: 2898 helix: 1.88 (0.16), residues: 1074 sheet: -0.01 (0.18), residues: 756 loop : -0.49 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 488 TYR 0.015 0.001 TYR B 235 PHE 0.020 0.002 PHE F 301 TRP 0.026 0.002 TRP A 92 HIS 0.002 0.000 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00317 (23644) covalent geometry : angle 0.45213 (31958) hydrogen bonds : bond 0.03013 ( 1092) hydrogen bonds : angle 4.16496 ( 3060) Misc. bond : bond 0.00144 ( 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 333 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 0.665 Fit side-chains REVERT: A 21 MET cc_start: 0.8309 (ptm) cc_final: 0.8051 (ptm) REVERT: A 77 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7401 (pt0) REVERT: A 232 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.7723 (mmtt) REVERT: A 336 GLU cc_start: 0.8196 (tp30) cc_final: 0.7820 (tt0) REVERT: A 357 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: A 390 ASN cc_start: 0.8501 (m-40) cc_final: 0.8255 (m110) REVERT: A 404 LYS cc_start: 0.8024 (mttt) cc_final: 0.7687 (mttm) REVERT: A 461 SER cc_start: 0.9185 (t) cc_final: 0.8952 (p) REVERT: B 128 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7679 (mm-30) REVERT: B 247 PHE cc_start: 0.7687 (m-80) cc_final: 0.7078 (t80) REVERT: B 357 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: B 362 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 449 MET cc_start: 0.8955 (mmm) cc_final: 0.8699 (mtt) REVERT: B 461 SER cc_start: 0.9357 (t) cc_final: 0.9112 (p) REVERT: B 471 MET cc_start: 0.8381 (mpp) cc_final: 0.8047 (mpp) REVERT: B 480 LYS cc_start: 0.8291 (mttp) cc_final: 0.7955 (mttp) REVERT: B 488 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7287 (mtm-85) REVERT: C 106 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8463 (tt) REVERT: C 128 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7636 (mm-30) REVERT: C 147 VAL cc_start: 0.8823 (m) cc_final: 0.8569 (m) REVERT: C 150 VAL cc_start: 0.7786 (m) cc_final: 0.7425 (p) REVERT: C 357 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: C 393 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6955 (mtm110) REVERT: C 487 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7292 (mt-10) REVERT: D 21 MET cc_start: 0.8342 (ptm) cc_final: 0.8048 (ptm) REVERT: D 77 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7417 (pt0) REVERT: D 162 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7383 (ttp80) REVERT: D 232 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.7770 (mmtt) REVERT: D 336 GLU cc_start: 0.8048 (tt0) cc_final: 0.7567 (tt0) REVERT: D 357 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7294 (pt0) REVERT: D 362 ILE cc_start: 0.8535 (mm) cc_final: 0.8314 (mp) REVERT: D 390 ASN cc_start: 0.8515 (m-40) cc_final: 0.8314 (m110) REVERT: D 461 SER cc_start: 0.9190 (t) cc_final: 0.8954 (p) REVERT: E 247 PHE cc_start: 0.7685 (m-80) cc_final: 0.7088 (t80) REVERT: E 257 ARG cc_start: 0.7180 (mmt180) cc_final: 0.6914 (mtm-85) REVERT: E 362 ILE cc_start: 0.8859 (mt) cc_final: 0.8553 (mt) REVERT: E 461 SER cc_start: 0.9379 (t) cc_final: 0.9134 (p) REVERT: E 488 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7248 (mtm-85) REVERT: F 106 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8455 (tt) REVERT: F 128 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7624 (mm-30) REVERT: F 147 VAL cc_start: 0.8812 (m) cc_final: 0.8576 (m) REVERT: F 150 VAL cc_start: 0.7801 (m) cc_final: 0.7443 (p) REVERT: F 357 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: F 393 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6946 (mtm110) REVERT: F 487 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7282 (mt-10) outliers start: 50 outliers final: 30 residues processed: 324 average time/residue: 0.7865 time to fit residues: 284.2175 Evaluate side-chains 316 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LYS 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 A residue 480 LYS Chi-restraints excluded: chain A residue 493 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 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 379 SER 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 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 F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 182 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 173 optimal weight: 9.9990 chunk 240 optimal weight: 0.0370 chunk 219 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 chunk 89 optimal weight: 0.0870 chunk 137 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 overall best weight: 2.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109458 restraints weight = 28994.488| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.03 r_work: 0.3189 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23656 Z= 0.172 Angle : 0.480 7.296 31958 Z= 0.261 Chirality : 0.043 0.146 3558 Planarity : 0.003 0.048 4090 Dihedral : 9.696 89.986 3612 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.13 % Allowed : 16.23 % Favored : 81.64 % 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: 0.68 (0.15), residues: 2898 helix: 1.81 (0.16), residues: 1080 sheet: -0.10 (0.18), residues: 780 loop : -0.46 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 393 TYR 0.018 0.002 TYR B 235 PHE 0.023 0.002 PHE F 301 TRP 0.027 0.002 TRP A 92 HIS 0.003 0.001 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00415 (23644) covalent geometry : angle 0.47974 (31958) hydrogen bonds : bond 0.03240 ( 1092) hydrogen bonds : angle 4.23102 ( 3060) Misc. bond : bond 0.00193 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8075.40 seconds wall clock time: 137 minutes 50.81 seconds (8270.81 seconds total)