Starting phenix.real_space_refine on Thu Sep 18 00:22:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikc_60655/09_2025/9ikc_60655.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikc_60655/09_2025/9ikc_60655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ikc_60655/09_2025/9ikc_60655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikc_60655/09_2025/9ikc_60655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ikc_60655/09_2025/9ikc_60655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikc_60655/09_2025/9ikc_60655.map" } resolution = 1.9 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 7878 2.51 5 N 2091 2.21 5 O 2508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12555 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4135 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 26, 'TRANS': 502} Chain: "B" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4135 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 26, 'TRANS': 502} Chain: "C" Number of atoms: 4135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4135 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 26, 'TRANS': 502} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Time building chain proxies: 3.27, per 1000 atoms: 0.26 Number of scatterers: 12555 At special positions: 0 Unit cell: (98.15, 98.8, 102.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2508 8.00 N 2091 7.00 C 7878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 616.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 33 sheets defined 20.4% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.544A pdb=" N SER A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 276 through 292 removed outlier: 3.795A pdb=" N ASP A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 455 through 464 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.548A pdb=" N SER B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 276 through 292 removed outlier: 3.748A pdb=" N ASP B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 455 through 465 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 512 through 517 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 183 through 186 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 276 through 292 removed outlier: 3.739A pdb=" N ASP C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 455 through 464 Processing helix chain 'C' and resid 491 through 495 Processing helix chain 'C' and resid 512 through 517 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 39 removed outlier: 3.914A pdb=" N ILE A 212 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN A 65 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 214 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N MET A 63 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE A 66 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 39 removed outlier: 3.914A pdb=" N ILE A 212 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN A 65 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 214 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N MET A 63 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 43 removed outlier: 6.863A pdb=" N ARG A 93 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 108 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 95 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A 106 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 97 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 236 removed outlier: 4.693A pdb=" N MET A 521 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE A 236 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG A 519 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 251 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 528 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS A 249 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.986A pdb=" N CYS A 249 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 528 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 251 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.451A pdb=" N ALA A 500 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 442 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 502 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET A 440 " --> pdb=" O ARG A 502 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 504 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE A 444 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AB1, first strand: chain 'A' and resid 317 through 320 removed outlier: 6.531A pdb=" N ASP A 324 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A 365 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE A 326 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG A 328 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR A 369 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP A 330 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A 362 " --> pdb=" O HIS A 383 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS A 383 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 364 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 381 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 366 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AB3, first strand: chain 'B' and resid 31 through 39 removed outlier: 3.908A pdb=" N ILE B 212 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASN B 65 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 214 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET B 63 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B 66 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 31 through 39 removed outlier: 3.908A pdb=" N ILE B 212 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASN B 65 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 214 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N MET B 63 " --> pdb=" O TYR B 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.842A pdb=" N ARG B 93 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER B 108 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 95 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU B 106 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 97 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB7, first strand: chain 'B' and resid 136 through 138 Processing sheet with id=AB8, first strand: chain 'B' and resid 224 through 233 removed outlier: 3.871A pdb=" N SER B 251 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 528 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS B 249 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 471 through 474 removed outlier: 6.974A pdb=" N CYS B 249 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL B 528 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 251 " --> pdb=" O ASN B 526 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.467A pdb=" N ALA B 500 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 442 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG B 502 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N MET B 440 " --> pdb=" O ARG B 502 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR B 504 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE B 444 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL B 448 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 293 through 296 Processing sheet with id=AC3, first strand: chain 'B' and resid 317 through 320 removed outlier: 6.535A pdb=" N ASP B 324 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ILE B 365 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHE B 326 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLY B 367 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG B 328 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR B 369 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP B 330 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B 362 " --> pdb=" O HIS B 383 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS B 383 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 364 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 381 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR B 366 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AC5, first strand: chain 'C' and resid 31 through 39 removed outlier: 3.914A pdb=" N ILE C 212 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN C 65 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR C 214 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N MET C 63 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 66 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 31 through 39 removed outlier: 3.914A pdb=" N ILE C 212 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN C 65 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR C 214 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N MET C 63 " --> pdb=" O TYR C 214 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 41 through 43 removed outlier: 6.822A pdb=" N ARG C 93 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER C 108 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL C 95 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU C 106 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL C 97 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC9, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AD1, first strand: chain 'C' and resid 224 through 236 removed outlier: 4.615A pdb=" N MET C 521 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE C 236 " --> pdb=" O ARG C 519 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG C 519 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER C 251 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 528 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS C 249 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 471 through 474 removed outlier: 6.969A pdb=" N CYS C 249 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 528 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER C 251 " --> pdb=" O ASN C 526 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 240 through 243 removed outlier: 6.460A pdb=" N ALA C 500 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 442 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG C 502 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET C 440 " --> pdb=" O ARG C 502 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR C 504 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE C 444 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL C 448 " --> pdb=" O PHE C 444 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 293 through 296 Processing sheet with id=AD5, first strand: chain 'C' and resid 317 through 320 removed outlier: 6.581A pdb=" N ASP C 324 " --> pdb=" O SER C 363 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE C 365 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE C 326 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY C 367 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG C 328 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR C 369 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP C 330 " --> pdb=" O TYR C 369 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE C 362 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS C 383 " --> pdb=" O PHE C 362 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 364 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA C 381 " --> pdb=" O ALA C 364 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR C 366 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 346 through 347 518 hydrogen bonds defined for protein. 1308 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: 2.30 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4068 1.34 - 1.46: 2837 1.46 - 1.58: 5635 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 12669 Sorted by residual: bond pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CG ARG C 350 " pdb=" CD ARG C 350 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.76e-01 bond pdb=" CG ARG B 350 " pdb=" CD ARG B 350 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.40e-01 bond pdb=" CB GLU B 305 " pdb=" CG GLU B 305 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 3.98e-01 bond pdb=" CB ASN B 491 " pdb=" CG ASN B 491 " ideal model delta sigma weight residual 1.516 1.531 -0.015 2.50e-02 1.60e+03 3.80e-01 ... (remaining 12664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 16993 1.56 - 3.13: 198 3.13 - 4.69: 33 4.69 - 6.26: 4 6.26 - 7.82: 1 Bond angle restraints: 17229 Sorted by residual: angle pdb=" CB MET B 32 " pdb=" CG MET B 32 " pdb=" SD MET B 32 " ideal model delta sigma weight residual 112.70 120.52 -7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " pdb=" NE ARG A 350 " ideal model delta sigma weight residual 112.00 117.62 -5.62 2.20e+00 2.07e-01 6.52e+00 angle pdb=" C ASP B 262 " pdb=" N ALA B 263 " pdb=" CA ALA B 263 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.61e+00 angle pdb=" C ASP A 262 " pdb=" N ALA A 263 " pdb=" CA ALA A 263 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" C SER A 480 " pdb=" N THR A 481 " pdb=" CA THR A 481 " ideal model delta sigma weight residual 121.54 125.98 -4.44 1.91e+00 2.74e-01 5.41e+00 ... (remaining 17224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6912 17.98 - 35.96: 526 35.96 - 53.94: 144 53.94 - 71.92: 51 71.92 - 89.89: 20 Dihedral angle restraints: 7653 sinusoidal: 2973 harmonic: 4680 Sorted by residual: dihedral pdb=" CG ARG B 377 " pdb=" CD ARG B 377 " pdb=" NE ARG B 377 " pdb=" CZ ARG B 377 " ideal model delta sinusoidal sigma weight residual -90.00 -39.94 -50.06 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA ASP A 162 " pdb=" CB ASP A 162 " pdb=" CG ASP A 162 " pdb=" OD1 ASP A 162 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CB GLU C 131 " pdb=" CG GLU C 131 " pdb=" CD GLU C 131 " pdb=" OE1 GLU C 131 " ideal model delta sinusoidal sigma weight residual 0.00 -89.89 89.89 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1065 0.026 - 0.053: 528 0.053 - 0.079: 182 0.079 - 0.105: 138 0.105 - 0.131: 88 Chirality restraints: 2001 Sorted by residual: chirality pdb=" CA VAL A 189 " pdb=" N VAL A 189 " pdb=" C VAL A 189 " pdb=" CB VAL A 189 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE B 320 " pdb=" N ILE B 320 " pdb=" C ILE B 320 " pdb=" CB ILE B 320 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL C 189 " pdb=" N VAL C 189 " pdb=" C VAL C 189 " pdb=" CB VAL C 189 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1998 not shown) Planarity restraints: 2223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 332 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO B 333 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO C 333 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 350 " 0.131 9.50e-02 1.11e+02 5.91e-02 2.73e+00 pdb=" NE ARG A 350 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 350 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 350 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 350 " 0.000 2.00e-02 2.50e+03 ... (remaining 2220 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1469 2.76 - 3.29: 11990 3.29 - 3.83: 22434 3.83 - 4.36: 26887 4.36 - 4.90: 44579 Nonbonded interactions: 107359 Sorted by model distance: nonbonded pdb=" OH TYR C 356 " pdb=" OD1 ASP C 389 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 356 " pdb=" OD1 ASP A 389 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 356 " pdb=" OD1 ASP B 389 " model vdw 2.231 3.040 nonbonded pdb=" O MET C 123 " pdb=" OG SER C 126 " model vdw 2.244 3.040 nonbonded pdb=" O MET B 123 " pdb=" OG SER B 126 " model vdw 2.253 3.040 ... (remaining 107354 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.120 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.002 0.035 12669 Z= 0.096 Angle : 0.474 7.820 17229 Z= 0.253 Chirality : 0.045 0.131 2001 Planarity : 0.004 0.059 2223 Dihedral : 15.818 89.894 4617 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.50 % Allowed : 13.48 % Favored : 86.02 % 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 aren not related in a simple way. whole: 0.18 (0.20), residues: 1581 helix: -0.18 (0.31), residues: 273 sheet: 1.02 (0.23), residues: 450 loop : -0.20 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 350 TYR 0.011 0.001 TYR A 516 PHE 0.011 0.001 PHE B 326 TRP 0.005 0.001 TRP C 397 HIS 0.002 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00199 (12669) covalent geometry : angle 0.47367 (17229) hydrogen bonds : bond 0.18278 ( 461) hydrogen bonds : angle 7.20026 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 228 time to evaluate : 0.497 Fit side-chains REVERT: A 192 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: A 217 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7419 (tttm) REVERT: B 192 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6643 (pm20) REVERT: B 433 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7937 (mptp) REVERT: C 217 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7350 (tttm) REVERT: C 222 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7450 (mmm160) REVERT: C 232 ARG cc_start: 0.8787 (tpt170) cc_final: 0.8426 (tpt170) REVERT: C 351 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7393 (mmtm) outliers start: 7 outliers final: 2 residues processed: 231 average time/residue: 0.8899 time to fit residues: 217.9760 Evaluate side-chains 230 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 225 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 192 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 overall best weight: 3.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.117673 restraints weight = 9113.710| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.17 r_work: 0.3214 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12669 Z= 0.224 Angle : 0.651 11.916 17229 Z= 0.354 Chirality : 0.051 0.157 2001 Planarity : 0.005 0.039 2223 Dihedral : 5.567 40.722 1743 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.00 % Allowed : 11.25 % Favored : 87.74 % 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 aren not related in a simple way. whole: -0.03 (0.20), residues: 1581 helix: -0.41 (0.29), residues: 270 sheet: 0.85 (0.23), residues: 441 loop : -0.28 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 377 TYR 0.019 0.002 TYR C 516 PHE 0.018 0.002 PHE C 419 TRP 0.008 0.003 TRP A 105 HIS 0.004 0.001 HIS C 341 Details of bonding type rmsd covalent geometry : bond 0.00475 (12669) covalent geometry : angle 0.65135 (17229) hydrogen bonds : bond 0.07289 ( 461) hydrogen bonds : angle 5.72951 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 215 MET cc_start: 0.8596 (mmm) cc_final: 0.8348 (mtm) REVERT: A 217 LYS cc_start: 0.7692 (tttp) cc_final: 0.7308 (tttm) REVERT: A 227 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: A 245 ASP cc_start: 0.8525 (m-30) cc_final: 0.8260 (m-30) REVERT: B 120 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: B 509 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: C 192 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: C 217 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7279 (tttm) REVERT: C 232 ARG cc_start: 0.8722 (tpt170) cc_final: 0.8393 (tpt170) REVERT: C 351 LYS cc_start: 0.7755 (mmmt) cc_final: 0.7411 (mmtm) outliers start: 14 outliers final: 7 residues processed: 239 average time/residue: 0.8648 time to fit residues: 219.4295 Evaluate side-chains 233 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 222 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 192 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116913 restraints weight = 9171.300| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.16 r_work: 0.3216 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12669 Z= 0.258 Angle : 0.686 12.856 17229 Z= 0.373 Chirality : 0.052 0.160 2001 Planarity : 0.005 0.038 2223 Dihedral : 5.309 32.671 1733 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.86 % Allowed : 10.32 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.20), residues: 1581 helix: -0.63 (0.28), residues: 270 sheet: 0.83 (0.23), residues: 435 loop : -0.38 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 471 TYR 0.020 0.003 TYR C 516 PHE 0.021 0.003 PHE A 419 TRP 0.010 0.003 TRP A 105 HIS 0.004 0.001 HIS C 341 Details of bonding type rmsd covalent geometry : bond 0.00548 (12669) covalent geometry : angle 0.68625 (17229) hydrogen bonds : bond 0.07542 ( 461) hydrogen bonds : angle 5.76662 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7187 (pptt) REVERT: A 192 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: A 217 LYS cc_start: 0.7718 (tttp) cc_final: 0.7292 (tttm) REVERT: A 227 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: A 245 ASP cc_start: 0.8541 (m-30) cc_final: 0.8298 (m-30) REVERT: B 120 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: B 192 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: B 227 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: B 509 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: C 58 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7184 (pptt) REVERT: C 130 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7809 (ttp-170) REVERT: C 192 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: C 217 LYS cc_start: 0.7714 (ttmt) cc_final: 0.7248 (tttm) REVERT: C 227 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8201 (mt-10) REVERT: C 232 ARG cc_start: 0.8779 (tpt170) cc_final: 0.8431 (tpt170) REVERT: C 351 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7416 (mmtm) outliers start: 26 outliers final: 9 residues processed: 243 average time/residue: 0.8985 time to fit residues: 231.0835 Evaluate side-chains 246 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117480 restraints weight = 9109.416| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.16 r_work: 0.3217 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12669 Z= 0.204 Angle : 0.631 13.133 17229 Z= 0.341 Chirality : 0.050 0.158 2001 Planarity : 0.005 0.037 2223 Dihedral : 5.192 31.369 1733 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 10.61 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.20), residues: 1581 helix: -0.55 (0.29), residues: 270 sheet: 0.72 (0.23), residues: 441 loop : -0.36 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 377 TYR 0.017 0.002 TYR C 516 PHE 0.016 0.002 PHE A 419 TRP 0.007 0.002 TRP A 105 HIS 0.004 0.001 HIS C 341 Details of bonding type rmsd covalent geometry : bond 0.00427 (12669) covalent geometry : angle 0.63066 (17229) hydrogen bonds : bond 0.06801 ( 461) hydrogen bonds : angle 5.60425 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7174 (pptt) REVERT: A 192 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6754 (pm20) REVERT: A 217 LYS cc_start: 0.7722 (tttp) cc_final: 0.7314 (tttm) REVERT: A 227 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: A 245 ASP cc_start: 0.8519 (m-30) cc_final: 0.8262 (m-30) REVERT: B 120 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: B 192 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: B 227 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: B 509 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: C 58 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7178 (pptt) REVERT: C 130 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7812 (ttp-170) REVERT: C 192 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: C 217 LYS cc_start: 0.7702 (ttmt) cc_final: 0.7223 (tttm) REVERT: C 227 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: C 232 ARG cc_start: 0.8772 (tpt170) cc_final: 0.8427 (tpt170) outliers start: 22 outliers final: 9 residues processed: 240 average time/residue: 0.8431 time to fit residues: 214.5060 Evaluate side-chains 243 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 0.0870 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119131 restraints weight = 9198.375| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.16 r_work: 0.3242 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12669 Z= 0.145 Angle : 0.567 13.625 17229 Z= 0.304 Chirality : 0.048 0.154 2001 Planarity : 0.004 0.036 2223 Dihedral : 4.934 28.051 1733 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.51 % Allowed : 11.04 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.20), residues: 1581 helix: -0.28 (0.29), residues: 270 sheet: 0.71 (0.23), residues: 441 loop : -0.32 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 377 TYR 0.015 0.001 TYR A 516 PHE 0.013 0.002 PHE B 483 TRP 0.006 0.002 TRP A 105 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00299 (12669) covalent geometry : angle 0.56678 (17229) hydrogen bonds : bond 0.05753 ( 461) hydrogen bonds : angle 5.31792 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: A 217 LYS cc_start: 0.7699 (tttp) cc_final: 0.7323 (tttm) REVERT: A 227 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: A 245 ASP cc_start: 0.8509 (m-30) cc_final: 0.8254 (m-30) REVERT: B 120 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: B 192 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: B 509 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: C 58 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7161 (pptt) REVERT: C 192 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: C 217 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7225 (tttm) REVERT: C 227 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: C 232 ARG cc_start: 0.8747 (tpt170) cc_final: 0.8389 (tpt170) outliers start: 21 outliers final: 10 residues processed: 237 average time/residue: 0.8474 time to fit residues: 212.8853 Evaluate side-chains 234 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117325 restraints weight = 9111.264| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.16 r_work: 0.3218 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12669 Z= 0.211 Angle : 0.640 13.072 17229 Z= 0.345 Chirality : 0.050 0.160 2001 Planarity : 0.005 0.037 2223 Dihedral : 5.177 31.472 1733 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.43 % Allowed : 11.18 % Favored : 87.38 % 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 aren not related in a simple way. whole: -0.15 (0.20), residues: 1581 helix: -0.43 (0.29), residues: 270 sheet: 0.71 (0.23), residues: 441 loop : -0.35 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.018 0.002 TYR C 516 PHE 0.018 0.002 PHE A 419 TRP 0.007 0.002 TRP A 105 HIS 0.004 0.001 HIS C 341 Details of bonding type rmsd covalent geometry : bond 0.00445 (12669) covalent geometry : angle 0.64038 (17229) hydrogen bonds : bond 0.06824 ( 461) hydrogen bonds : angle 5.57892 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6742 (pm20) REVERT: A 217 LYS cc_start: 0.7722 (tttp) cc_final: 0.7306 (tttm) REVERT: A 227 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: A 245 ASP cc_start: 0.8516 (m-30) cc_final: 0.8271 (m-30) REVERT: B 120 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: B 192 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: B 509 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: C 58 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7185 (pptt) REVERT: C 192 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: C 217 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7213 (tttm) REVERT: C 227 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: C 232 ARG cc_start: 0.8777 (tpt170) cc_final: 0.8429 (tpt170) outliers start: 20 outliers final: 9 residues processed: 233 average time/residue: 0.8613 time to fit residues: 212.8019 Evaluate side-chains 238 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119474 restraints weight = 9178.987| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.16 r_work: 0.3229 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12669 Z= 0.140 Angle : 0.566 13.662 17229 Z= 0.301 Chirality : 0.048 0.154 2001 Planarity : 0.004 0.043 2223 Dihedral : 4.893 27.641 1733 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.43 % Allowed : 11.33 % Favored : 87.24 % 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 aren not related in a simple way. whole: -0.05 (0.20), residues: 1581 helix: -0.21 (0.30), residues: 270 sheet: 0.71 (0.24), residues: 441 loop : -0.30 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 350 TYR 0.015 0.001 TYR A 516 PHE 0.013 0.001 PHE B 483 TRP 0.005 0.002 TRP A 105 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00289 (12669) covalent geometry : angle 0.56635 (17229) hydrogen bonds : bond 0.05574 ( 461) hydrogen bonds : angle 5.24767 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: A 217 LYS cc_start: 0.7704 (tttp) cc_final: 0.7366 (tttm) REVERT: A 227 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: A 245 ASP cc_start: 0.8512 (m-30) cc_final: 0.8264 (m-30) REVERT: B 120 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: B 192 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: B 509 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: C 58 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7175 (pptt) REVERT: C 192 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: C 217 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7257 (tttm) REVERT: C 227 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: C 232 ARG cc_start: 0.8737 (tpt170) cc_final: 0.8414 (tpt170) outliers start: 20 outliers final: 6 residues processed: 230 average time/residue: 0.8709 time to fit residues: 212.1749 Evaluate side-chains 230 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 45 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115948 restraints weight = 9097.904| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.15 r_work: 0.3196 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12669 Z= 0.319 Angle : 0.755 12.848 17229 Z= 0.409 Chirality : 0.054 0.160 2001 Planarity : 0.006 0.047 2223 Dihedral : 5.434 34.065 1733 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.36 % Allowed : 11.18 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.20), residues: 1581 helix: -0.69 (0.28), residues: 270 sheet: 0.69 (0.23), residues: 441 loop : -0.39 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 350 TYR 0.021 0.003 TYR C 516 PHE 0.025 0.003 PHE A 419 TRP 0.012 0.003 TRP A 105 HIS 0.005 0.002 HIS C 507 Details of bonding type rmsd covalent geometry : bond 0.00685 (12669) covalent geometry : angle 0.75466 (17229) hydrogen bonds : bond 0.07961 ( 461) hydrogen bonds : angle 5.81851 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: A 217 LYS cc_start: 0.7748 (tttp) cc_final: 0.7328 (tttm) REVERT: A 227 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: B 120 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: B 192 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: B 509 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: C 39 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8330 (mp-120) REVERT: C 58 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7238 (pptt) REVERT: C 192 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: C 217 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7198 (tttm) REVERT: C 232 ARG cc_start: 0.8799 (tpt170) cc_final: 0.8450 (tpt170) outliers start: 19 outliers final: 9 residues processed: 228 average time/residue: 0.8789 time to fit residues: 212.5194 Evaluate side-chains 234 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 218 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 201 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118849 restraints weight = 9133.511| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.16 r_work: 0.3238 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12669 Z= 0.156 Angle : 0.596 13.519 17229 Z= 0.318 Chirality : 0.048 0.155 2001 Planarity : 0.004 0.060 2223 Dihedral : 5.040 29.328 1733 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.08 % Allowed : 11.76 % Favored : 87.17 % 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 aren not related in a simple way. whole: -0.14 (0.20), residues: 1581 helix: -0.35 (0.29), residues: 270 sheet: 0.68 (0.23), residues: 441 loop : -0.35 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 350 TYR 0.016 0.002 TYR B 516 PHE 0.013 0.002 PHE B 483 TRP 0.006 0.002 TRP A 105 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00325 (12669) covalent geometry : angle 0.59608 (17229) hydrogen bonds : bond 0.05915 ( 461) hydrogen bonds : angle 5.35014 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: A 217 LYS cc_start: 0.7708 (tttp) cc_final: 0.7309 (tttm) REVERT: A 227 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: A 245 ASP cc_start: 0.8502 (m-30) cc_final: 0.8255 (m-30) REVERT: B 120 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: B 192 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6972 (pm20) REVERT: B 509 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: C 58 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7150 (pptt) REVERT: C 192 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: C 217 LYS cc_start: 0.7675 (ttmt) cc_final: 0.7208 (tttm) REVERT: C 232 ARG cc_start: 0.8747 (tpt170) cc_final: 0.8400 (tpt170) outliers start: 15 outliers final: 7 residues processed: 228 average time/residue: 0.9059 time to fit residues: 218.7307 Evaluate side-chains 230 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 90 optimal weight: 0.0980 chunk 144 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118156 restraints weight = 9198.488| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.16 r_work: 0.3230 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12669 Z= 0.177 Angle : 0.622 13.305 17229 Z= 0.332 Chirality : 0.049 0.158 2001 Planarity : 0.004 0.056 2223 Dihedral : 5.087 29.908 1733 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.15 % Allowed : 11.76 % Favored : 87.10 % 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 aren not related in a simple way. whole: -0.13 (0.20), residues: 1581 helix: -0.37 (0.29), residues: 270 sheet: 0.68 (0.23), residues: 441 loop : -0.33 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 350 TYR 0.016 0.002 TYR A 516 PHE 0.014 0.002 PHE A 419 TRP 0.007 0.002 TRP A 105 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00372 (12669) covalent geometry : angle 0.62192 (17229) hydrogen bonds : bond 0.06264 ( 461) hydrogen bonds : angle 5.42916 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3162 Ramachandran restraints generated. 1581 Oldfield, 0 Emsley, 1581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6736 (pm20) REVERT: A 217 LYS cc_start: 0.7715 (tttp) cc_final: 0.7313 (tttm) REVERT: A 227 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: A 245 ASP cc_start: 0.8499 (m-30) cc_final: 0.8253 (m-30) REVERT: B 120 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: B 192 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6978 (pm20) REVERT: B 509 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: C 58 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7156 (pptt) REVERT: C 192 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: C 217 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7220 (tttm) REVERT: C 227 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: C 232 ARG cc_start: 0.8761 (tpt170) cc_final: 0.8413 (tpt170) outliers start: 16 outliers final: 7 residues processed: 223 average time/residue: 0.9239 time to fit residues: 218.0243 Evaluate side-chains 228 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 401 ARG Chi-restraints excluded: chain B residue 509 GLU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 227 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119336 restraints weight = 9144.574| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.16 r_work: 0.3246 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12669 Z= 0.148 Angle : 0.591 13.526 17229 Z= 0.313 Chirality : 0.048 0.155 2001 Planarity : 0.004 0.056 2223 Dihedral : 4.937 27.787 1733 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.15 % Allowed : 11.76 % Favored : 87.10 % 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 aren not related in a simple way. whole: -0.07 (0.20), residues: 1581 helix: -0.24 (0.29), residues: 270 sheet: 0.69 (0.23), residues: 441 loop : -0.30 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 350 TYR 0.015 0.001 TYR B 516 PHE 0.013 0.002 PHE B 483 TRP 0.006 0.002 TRP A 105 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00310 (12669) covalent geometry : angle 0.59116 (17229) hydrogen bonds : bond 0.05678 ( 461) hydrogen bonds : angle 5.26989 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7439.96 seconds wall clock time: 127 minutes 0.83 seconds (7620.83 seconds total)