Starting phenix.real_space_refine on Thu Mar 5 00:29:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7squ_25395/03_2026/7squ_25395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7squ_25395/03_2026/7squ_25395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7squ_25395/03_2026/7squ_25395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7squ_25395/03_2026/7squ_25395.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7squ_25395/03_2026/7squ_25395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7squ_25395/03_2026/7squ_25395.map" } resolution = 2.6 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= 0.003 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 84 5.16 5 C 11256 2.51 5 N 3104 2.21 5 O 3412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17856 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4237 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 32, 'TRANS': 509} Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 180 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 47 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Restraints were copied for chains: D, G, J, E, H, K, F, I, L Time building chain proxies: 3.81, per 1000 atoms: 0.21 Number of scatterers: 17856 At special positions: 0 Unit cell: (147.538, 147.538, 91.0975, 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 84 16.00 O 3412 8.00 N 3104 7.00 C 11256 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: 1.04 Conformation dependent library (CDL) restraints added in 693.8 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4240 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 20 sheets defined 41.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.635A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA A 231 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.541A pdb=" N ALA A 375 " --> pdb=" O ASN A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 529 through 546 Processing helix chain 'A' and resid 561 through 575 Processing helix chain 'B' and resid 596 through 601 removed outlier: 4.344A pdb=" N ALA B 600 " --> pdb=" O MET B 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 596 through 601' Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.856A pdb=" N ILE B 610 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 611 " --> pdb=" O GLY B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 611' Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 64 through 78 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.634A pdb=" N GLY D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 221 removed outlier: 6.277A pdb=" N ASP D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA D 231 " --> pdb=" O GLY D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 351 Processing helix chain 'D' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU D 360 " --> pdb=" O TRP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.541A pdb=" N ALA D 375 " --> pdb=" O ASN D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 448 through 462 removed outlier: 3.540A pdb=" N LYS D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 512 through 525 Processing helix chain 'D' and resid 529 through 546 Processing helix chain 'D' and resid 561 through 575 Processing helix chain 'E' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA E 600 " --> pdb=" O MET E 596 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 601 " --> pdb=" O ALA E 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 596 through 601' Processing helix chain 'E' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE E 610 " --> pdb=" O SER E 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR E 611 " --> pdb=" O GLY E 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 607 through 611' Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'G' and resid 64 through 78 Processing helix chain 'G' and resid 148 through 153 Processing helix chain 'G' and resid 154 through 170 Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.635A pdb=" N GLY G 175 " --> pdb=" O LYS G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.568A pdb=" N ALA G 231 " --> pdb=" O GLY G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 351 Processing helix chain 'G' and resid 356 through 364 removed outlier: 4.320A pdb=" N LEU G 360 " --> pdb=" O TRP G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 367 No H-bonds generated for 'chain 'G' and resid 365 through 367' Processing helix chain 'G' and resid 372 through 375 removed outlier: 3.541A pdb=" N ALA G 375 " --> pdb=" O ASN G 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 372 through 375' Processing helix chain 'G' and resid 376 through 381 Processing helix chain 'G' and resid 394 through 403 Processing helix chain 'G' and resid 422 through 427 Processing helix chain 'G' and resid 427 through 432 Processing helix chain 'G' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS G 452 " --> pdb=" O SER G 448 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR G 462 " --> pdb=" O PHE G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 470 Processing helix chain 'G' and resid 500 through 502 No H-bonds generated for 'chain 'G' and resid 500 through 502' Processing helix chain 'G' and resid 503 through 511 Processing helix chain 'G' and resid 512 through 525 Processing helix chain 'G' and resid 529 through 546 Processing helix chain 'G' and resid 561 through 575 Processing helix chain 'H' and resid 596 through 601 removed outlier: 4.345A pdb=" N ALA H 600 " --> pdb=" O MET H 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG H 601 " --> pdb=" O ALA H 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 596 through 601' Processing helix chain 'H' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE H 610 " --> pdb=" O SER H 607 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR H 611 " --> pdb=" O GLY H 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 607 through 611' Processing helix chain 'J' and resid 45 through 47 No H-bonds generated for 'chain 'J' and resid 45 through 47' Processing helix chain 'J' and resid 48 through 53 Processing helix chain 'J' and resid 64 through 78 Processing helix chain 'J' and resid 148 through 153 Processing helix chain 'J' and resid 154 through 170 Processing helix chain 'J' and resid 171 through 175 removed outlier: 3.635A pdb=" N GLY J 175 " --> pdb=" O LYS J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 221 removed outlier: 6.277A pdb=" N ASP J 218 " --> pdb=" O ILE J 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS J 219 " --> pdb=" O ARG J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA J 231 " --> pdb=" O GLY J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 351 Processing helix chain 'J' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU J 360 " --> pdb=" O TRP J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 367 No H-bonds generated for 'chain 'J' and resid 365 through 367' Processing helix chain 'J' and resid 372 through 375 removed outlier: 3.542A pdb=" N ALA J 375 " --> pdb=" O ASN J 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 372 through 375' Processing helix chain 'J' and resid 376 through 381 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 422 through 427 Processing helix chain 'J' and resid 427 through 432 Processing helix chain 'J' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS J 452 " --> pdb=" O SER J 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR J 462 " --> pdb=" O PHE J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 470 Processing helix chain 'J' and resid 500 through 502 No H-bonds generated for 'chain 'J' and resid 500 through 502' Processing helix chain 'J' and resid 503 through 511 Processing helix chain 'J' and resid 512 through 525 Processing helix chain 'J' and resid 529 through 546 Processing helix chain 'J' and resid 561 through 575 Processing helix chain 'K' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA K 600 " --> pdb=" O MET K 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG K 601 " --> pdb=" O ALA K 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 596 through 601' Processing helix chain 'K' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE K 610 " --> pdb=" O SER K 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR K 611 " --> pdb=" O GLY K 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 607 through 611' Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 91 removed outlier: 6.947A pdb=" N ASN A 115 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG A 178 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 117 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA A 180 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 119 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 182 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 121 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 7.188A pdb=" N THR A 480 " --> pdb=" O ASP A 559 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP A 559 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN A 482 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 557 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS A 488 " --> pdb=" O GLN A 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN A 551 " --> pdb=" O HIS A 488 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE A 412 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER A 325 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 14.477A pdb=" N TYR A 327 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR A 285 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA A 326 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 283 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 281 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN A 278 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 268 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 280 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A 266 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 282 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 234 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.518A pdb=" N ASP A 248 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 91 removed outlier: 6.947A pdb=" N ASN D 115 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG D 178 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE D 117 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA D 180 " --> pdb=" O PHE D 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY D 119 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 182 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL D 121 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 134 through 137 Processing sheet with id=AA8, first strand: chain 'D' and resid 496 through 498 removed outlier: 7.188A pdb=" N THR D 480 " --> pdb=" O ASP D 559 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP D 559 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN D 482 " --> pdb=" O ARG D 557 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 557 " --> pdb=" O ASN D 482 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HIS D 488 " --> pdb=" O GLN D 551 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN D 551 " --> pdb=" O HIS D 488 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE D 412 " --> pdb=" O PHE D 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER D 325 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 14.478A pdb=" N TYR D 327 " --> pdb=" O PRO D 417 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR D 285 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA D 326 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA D 283 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 281 " --> pdb=" O PRO D 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN D 278 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 268 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG D 280 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN D 266 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 282 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 234 " --> pdb=" O ARG D 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.518A pdb=" N ASP D 248 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 305 through 306 Processing sheet with id=AB2, first strand: chain 'G' and resid 87 through 91 removed outlier: 6.947A pdb=" N ASN G 115 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ARG G 178 " --> pdb=" O ASN G 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE G 117 " --> pdb=" O ARG G 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA G 180 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY G 119 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU G 182 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL G 121 " --> pdb=" O LEU G 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 134 through 137 Processing sheet with id=AB4, first strand: chain 'G' and resid 496 through 498 removed outlier: 7.188A pdb=" N THR G 480 " --> pdb=" O ASP G 559 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ASP G 559 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN G 482 " --> pdb=" O ARG G 557 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG G 557 " --> pdb=" O ASN G 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS G 488 " --> pdb=" O GLN G 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN G 551 " --> pdb=" O HIS G 488 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE G 412 " --> pdb=" O PHE G 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER G 325 " --> pdb=" O ASP G 415 " (cutoff:3.500A) removed outlier: 14.478A pdb=" N TYR G 327 " --> pdb=" O PRO G 417 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR G 285 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA G 326 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA G 283 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU G 281 " --> pdb=" O PRO G 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN G 278 " --> pdb=" O ILE G 268 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE G 268 " --> pdb=" O GLN G 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG G 280 " --> pdb=" O ASN G 266 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN G 266 " --> pdb=" O ARG G 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 282 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN G 234 " --> pdb=" O ARG G 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP G 248 " --> pdb=" O VAL G 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 305 through 306 Processing sheet with id=AB7, first strand: chain 'J' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN J 115 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG J 178 " --> pdb=" O ASN J 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE J 117 " --> pdb=" O ARG J 178 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA J 180 " --> pdb=" O PHE J 117 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY J 119 " --> pdb=" O ALA J 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU J 182 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL J 121 " --> pdb=" O LEU J 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 134 through 137 Processing sheet with id=AB9, first strand: chain 'J' and resid 496 through 498 removed outlier: 7.189A pdb=" N THR J 480 " --> pdb=" O ASP J 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP J 559 " --> pdb=" O THR J 480 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASN J 482 " --> pdb=" O ARG J 557 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG J 557 " --> pdb=" O ASN J 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS J 488 " --> pdb=" O GLN J 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN J 551 " --> pdb=" O HIS J 488 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE J 412 " --> pdb=" O PHE J 560 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER J 325 " --> pdb=" O ASP J 415 " (cutoff:3.500A) removed outlier: 14.478A pdb=" N TYR J 327 " --> pdb=" O PRO J 417 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR J 285 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA J 326 " --> pdb=" O ALA J 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA J 283 " --> pdb=" O ALA J 326 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU J 281 " --> pdb=" O PRO J 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN J 278 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE J 268 " --> pdb=" O GLN J 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG J 280 " --> pdb=" O ASN J 266 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN J 266 " --> pdb=" O ARG J 280 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL J 282 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN J 234 " --> pdb=" O ARG J 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 248 through 249 removed outlier: 3.518A pdb=" N ASP J 248 " --> pdb=" O VAL J 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 305 through 306 772 hydrogen bonds defined for protein. 2160 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: 2.97 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5887 1.33 - 1.45: 2406 1.45 - 1.57: 9783 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 18240 Sorted by residual: bond pdb=" N VAL J 66 " pdb=" CA VAL J 66 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" N VAL A 66 " pdb=" CA VAL A 66 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" N VAL D 66 " pdb=" CA VAL D 66 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.42e+00 bond pdb=" N THR J 61 " pdb=" CA THR J 61 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.31e-02 5.83e+03 7.16e+00 bond pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.31e-02 5.83e+03 7.13e+00 ... (remaining 18235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 23081 1.24 - 2.49: 1449 2.49 - 3.73: 234 3.73 - 4.97: 48 4.97 - 6.21: 16 Bond angle restraints: 24828 Sorted by residual: angle pdb=" N THR J 437 " pdb=" CA THR J 437 " pdb=" C THR J 437 " ideal model delta sigma weight residual 110.20 103.99 6.21 1.58e+00 4.01e-01 1.55e+01 angle pdb=" N THR A 437 " pdb=" CA THR A 437 " pdb=" C THR A 437 " ideal model delta sigma weight residual 110.20 104.00 6.20 1.58e+00 4.01e-01 1.54e+01 angle pdb=" N THR G 437 " pdb=" CA THR G 437 " pdb=" C THR G 437 " ideal model delta sigma weight residual 110.20 104.00 6.20 1.58e+00 4.01e-01 1.54e+01 angle pdb=" N THR D 437 " pdb=" CA THR D 437 " pdb=" C THR D 437 " ideal model delta sigma weight residual 110.20 104.01 6.19 1.58e+00 4.01e-01 1.54e+01 angle pdb=" CA GLY G 62 " pdb=" C GLY G 62 " pdb=" O GLY G 62 " ideal model delta sigma weight residual 122.65 118.10 4.55 1.28e+00 6.10e-01 1.26e+01 ... (remaining 24823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 9453 16.10 - 32.21: 1075 32.21 - 48.31: 304 48.31 - 64.42: 64 64.42 - 80.52: 36 Dihedral angle restraints: 10932 sinusoidal: 4308 harmonic: 6624 Sorted by residual: dihedral pdb=" N GLU J 570 " pdb=" CA GLU J 570 " pdb=" CB GLU J 570 " pdb=" CG GLU J 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.27 -57.73 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLU A 570 " pdb=" CA GLU A 570 " pdb=" CB GLU A 570 " pdb=" CG GLU A 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.27 -57.73 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLU G 570 " pdb=" CA GLU G 570 " pdb=" CB GLU G 570 " pdb=" CG GLU G 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.30 -57.70 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 10929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1233 0.033 - 0.065: 882 0.065 - 0.098: 465 0.098 - 0.131: 156 0.131 - 0.164: 44 Chirality restraints: 2780 Sorted by residual: chirality pdb=" CA PRO D 513 " pdb=" N PRO D 513 " pdb=" C PRO D 513 " pdb=" CB PRO D 513 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA PRO A 513 " pdb=" N PRO A 513 " pdb=" C PRO A 513 " pdb=" CB PRO A 513 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA PRO G 513 " pdb=" N PRO G 513 " pdb=" C PRO G 513 " pdb=" CB PRO G 513 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 2777 not shown) Planarity restraints: 3272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 335 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO D 336 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 336 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 336 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 335 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO J 336 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO J 336 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 336 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 335 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 336 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.030 5.00e-02 4.00e+02 ... (remaining 3269 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4004 2.79 - 3.32: 15043 3.32 - 3.84: 27177 3.84 - 4.37: 32521 4.37 - 4.90: 56217 Nonbonded interactions: 134962 Sorted by model distance: nonbonded pdb=" NE2 GLN G 137 " pdb=" OD1 ASN G 142 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN D 137 " pdb=" OD1 ASN D 142 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN J 137 " pdb=" OD1 ASN J 142 " model vdw 2.259 3.120 nonbonded pdb=" NE2 GLN A 137 " pdb=" OD1 ASN A 142 " model vdw 2.259 3.120 nonbonded pdb=" O ARG A 525 " pdb=" NH2 ARG A 533 " model vdw 2.337 3.120 ... (remaining 134957 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.370 Find NCS groups from input model: 0.140 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.010 0.053 18240 Z= 0.408 Angle : 0.698 6.214 24828 Z= 0.406 Chirality : 0.055 0.164 2780 Planarity : 0.005 0.054 3272 Dihedral : 15.781 80.523 6692 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.04 % Allowed : 15.66 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.17), residues: 2268 helix: 1.96 (0.20), residues: 772 sheet: 1.14 (0.22), residues: 536 loop : -0.01 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 147 TYR 0.016 0.002 TYR D 455 PHE 0.011 0.002 PHE G 339 TRP 0.012 0.003 TRP A 424 HIS 0.005 0.001 HIS G 491 Details of bonding type rmsd covalent geometry : bond 0.00969 (18240) covalent geometry : angle 0.69777 (24828) hydrogen bonds : bond 0.19583 ( 772) hydrogen bonds : angle 6.13495 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 326 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.8813 (mtm) cc_final: 0.8345 (mtp) REVERT: A 384 VAL cc_start: 0.7762 (t) cc_final: 0.7515 (t) REVERT: A 452 LYS cc_start: 0.8671 (mttt) cc_final: 0.8433 (mtmm) REVERT: D 106 MET cc_start: 0.8772 (mtm) cc_final: 0.8311 (mtp) REVERT: D 384 VAL cc_start: 0.7760 (t) cc_final: 0.7519 (t) REVERT: D 452 LYS cc_start: 0.8669 (mttt) cc_final: 0.8431 (mtmm) REVERT: G 106 MET cc_start: 0.8754 (mtm) cc_final: 0.8292 (mtp) REVERT: G 384 VAL cc_start: 0.7768 (t) cc_final: 0.7528 (t) REVERT: G 452 LYS cc_start: 0.8675 (mttt) cc_final: 0.8464 (mtmm) REVERT: J 106 MET cc_start: 0.8799 (mtm) cc_final: 0.8330 (mtp) REVERT: J 384 VAL cc_start: 0.7774 (t) cc_final: 0.7530 (t) REVERT: J 452 LYS cc_start: 0.8673 (mttt) cc_final: 0.8437 (mtmm) outliers start: 20 outliers final: 4 residues processed: 338 average time/residue: 0.7740 time to fit residues: 284.8469 Evaluate side-chains 216 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 212 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain J residue 60 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.3980 chunk 212 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.113885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.079729 restraints weight = 34182.060| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.65 r_work: 0.3041 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18240 Z= 0.133 Angle : 0.570 8.759 24828 Z= 0.300 Chirality : 0.044 0.145 2780 Planarity : 0.005 0.047 3272 Dihedral : 4.023 19.186 2532 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.77 % Allowed : 18.16 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.17), residues: 2268 helix: 1.97 (0.20), residues: 772 sheet: 0.80 (0.21), residues: 556 loop : 0.20 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 456 TYR 0.013 0.001 TYR A 292 PHE 0.016 0.001 PHE J 401 TRP 0.020 0.002 TRP A 519 HIS 0.003 0.001 HIS D 114 Details of bonding type rmsd covalent geometry : bond 0.00298 (18240) covalent geometry : angle 0.56984 (24828) hydrogen bonds : bond 0.05167 ( 772) hydrogen bonds : angle 4.89607 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.428 Fit side-chains REVERT: A 106 MET cc_start: 0.9075 (mtm) cc_final: 0.8487 (mtp) REVERT: A 292 TYR cc_start: 0.8037 (t80) cc_final: 0.7596 (t80) REVERT: A 378 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6127 (mpt) REVERT: A 452 LYS cc_start: 0.8787 (mttt) cc_final: 0.8585 (mtmm) REVERT: A 507 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.6971 (mpm) REVERT: A 521 ASP cc_start: 0.8418 (m-30) cc_final: 0.8095 (m-30) REVERT: D 106 MET cc_start: 0.9059 (mtm) cc_final: 0.8474 (mtp) REVERT: D 292 TYR cc_start: 0.8018 (t80) cc_final: 0.7590 (t80) REVERT: D 378 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.6122 (mpt) REVERT: D 452 LYS cc_start: 0.8789 (mttt) cc_final: 0.8586 (mtmm) REVERT: D 507 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6985 (mpm) REVERT: D 521 ASP cc_start: 0.8406 (m-30) cc_final: 0.8101 (m-30) REVERT: D 574 ASP cc_start: 0.8114 (m-30) cc_final: 0.7910 (m-30) REVERT: G 106 MET cc_start: 0.9076 (mtm) cc_final: 0.8497 (mtp) REVERT: G 292 TYR cc_start: 0.8020 (t80) cc_final: 0.7591 (t80) REVERT: G 378 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.6134 (mpt) REVERT: G 452 LYS cc_start: 0.8800 (mttt) cc_final: 0.8595 (mtmm) REVERT: G 507 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7104 (mpm) REVERT: G 521 ASP cc_start: 0.8409 (m-30) cc_final: 0.8113 (m-30) REVERT: G 574 ASP cc_start: 0.8171 (m-30) cc_final: 0.7967 (m-30) REVERT: J 106 MET cc_start: 0.9082 (mtm) cc_final: 0.8491 (mtp) REVERT: J 292 TYR cc_start: 0.8076 (t80) cc_final: 0.7653 (t80) REVERT: J 378 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.6126 (mpt) REVERT: J 452 LYS cc_start: 0.8798 (mttt) cc_final: 0.8595 (mtmm) REVERT: J 507 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7102 (mpm) REVERT: J 521 ASP cc_start: 0.8417 (m-30) cc_final: 0.8057 (m-30) REVERT: J 574 ASP cc_start: 0.8152 (m-30) cc_final: 0.7951 (m-30) outliers start: 53 outliers final: 4 residues processed: 269 average time/residue: 0.7741 time to fit residues: 227.3342 Evaluate side-chains 219 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 507 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 507 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 507 MET Chi-restraints excluded: chain J residue 545 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 44 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 6 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076236 restraints weight = 34267.298| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.61 r_work: 0.2950 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18240 Z= 0.174 Angle : 0.564 9.297 24828 Z= 0.294 Chirality : 0.045 0.155 2780 Planarity : 0.005 0.045 3272 Dihedral : 3.945 16.912 2524 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.18 % Allowed : 19.47 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2268 helix: 1.97 (0.20), residues: 776 sheet: 0.74 (0.22), residues: 548 loop : 0.07 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 533 TYR 0.011 0.002 TYR D 472 PHE 0.022 0.001 PHE A 401 TRP 0.014 0.002 TRP J 519 HIS 0.002 0.001 HIS D 114 Details of bonding type rmsd covalent geometry : bond 0.00419 (18240) covalent geometry : angle 0.56424 (24828) hydrogen bonds : bond 0.05618 ( 772) hydrogen bonds : angle 4.72263 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7908 (mpp80) REVERT: A 354 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7546 (tpt) REVERT: A 403 GLN cc_start: 0.8566 (mt0) cc_final: 0.7940 (tp-100) REVERT: A 452 LYS cc_start: 0.8816 (mttt) cc_final: 0.8602 (mtmm) REVERT: A 521 ASP cc_start: 0.8569 (m-30) cc_final: 0.8224 (m-30) REVERT: A 570 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: D 51 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7913 (mpp80) REVERT: D 354 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7543 (tpt) REVERT: D 403 GLN cc_start: 0.8550 (mt0) cc_final: 0.7944 (tp-100) REVERT: D 452 LYS cc_start: 0.8800 (mttt) cc_final: 0.8584 (mtmm) REVERT: D 521 ASP cc_start: 0.8563 (m-30) cc_final: 0.8112 (m-30) REVERT: D 570 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: D 574 ASP cc_start: 0.8281 (m-30) cc_final: 0.8073 (m-30) REVERT: G 51 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7903 (mpp80) REVERT: G 354 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7553 (tpt) REVERT: G 403 GLN cc_start: 0.8544 (mt0) cc_final: 0.7936 (tp-100) REVERT: G 452 LYS cc_start: 0.8803 (mttt) cc_final: 0.8583 (mtmm) REVERT: G 521 ASP cc_start: 0.8572 (m-30) cc_final: 0.8228 (m-30) REVERT: G 570 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: G 574 ASP cc_start: 0.8274 (m-30) cc_final: 0.8065 (m-30) REVERT: J 51 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7909 (mpp80) REVERT: J 354 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7530 (tpt) REVERT: J 403 GLN cc_start: 0.8566 (mt0) cc_final: 0.7933 (tp-100) REVERT: J 452 LYS cc_start: 0.8805 (mttt) cc_final: 0.8589 (mtmm) REVERT: J 521 ASP cc_start: 0.8506 (m-30) cc_final: 0.8150 (m-30) REVERT: J 570 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: J 574 ASP cc_start: 0.8284 (m-30) cc_final: 0.8078 (m-30) REVERT: K 593 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.7067 (mtm110) outliers start: 61 outliers final: 20 residues processed: 253 average time/residue: 0.7744 time to fit residues: 214.3390 Evaluate side-chains 234 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 366 ARG Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 51 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 366 ARG Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 51 ARG Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 366 ARG Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 108 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN D 65 GLN G 65 GLN J 65 GLN J 140 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.107255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.073034 restraints weight = 34460.329| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.55 r_work: 0.2915 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 18240 Z= 0.336 Angle : 0.681 9.179 24828 Z= 0.358 Chirality : 0.051 0.167 2780 Planarity : 0.006 0.097 3272 Dihedral : 4.483 18.103 2524 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.55 % Allowed : 19.52 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2268 helix: 1.51 (0.19), residues: 764 sheet: 0.39 (0.22), residues: 548 loop : -0.34 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 593 TYR 0.019 0.002 TYR D 506 PHE 0.021 0.002 PHE A 401 TRP 0.013 0.003 TRP D 549 HIS 0.012 0.001 HIS J 140 Details of bonding type rmsd covalent geometry : bond 0.00822 (18240) covalent geometry : angle 0.68073 (24828) hydrogen bonds : bond 0.07220 ( 772) hydrogen bonds : angle 5.05652 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 191 time to evaluate : 0.517 Fit side-chains REVERT: A 188 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: A 354 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7618 (tpt) REVERT: A 403 GLN cc_start: 0.8743 (mt0) cc_final: 0.8162 (tp-100) REVERT: A 521 ASP cc_start: 0.8735 (m-30) cc_final: 0.8307 (m-30) REVERT: A 570 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: D 188 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: D 354 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7667 (tpt) REVERT: D 403 GLN cc_start: 0.8740 (mt0) cc_final: 0.8151 (tp-100) REVERT: D 521 ASP cc_start: 0.8703 (m-30) cc_final: 0.8277 (m-30) REVERT: D 570 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: G 188 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: G 354 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7646 (tpt) REVERT: G 403 GLN cc_start: 0.8737 (mt0) cc_final: 0.8111 (tp-100) REVERT: G 507 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7367 (mpm) REVERT: G 521 ASP cc_start: 0.8730 (m-30) cc_final: 0.8310 (m-30) REVERT: G 570 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: G 574 ASP cc_start: 0.8459 (m-30) cc_final: 0.8254 (m-30) REVERT: J 188 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: J 354 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7641 (tpt) REVERT: J 403 GLN cc_start: 0.8742 (mt0) cc_final: 0.8139 (tp-100) REVERT: J 507 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7324 (mpm) REVERT: J 521 ASP cc_start: 0.8628 (m-30) cc_final: 0.8202 (m-30) REVERT: J 570 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: J 574 ASP cc_start: 0.8456 (m-30) cc_final: 0.8251 (m-30) REVERT: K 593 ARG cc_start: 0.7809 (mtp-110) cc_final: 0.7238 (mtm110) outliers start: 68 outliers final: 15 residues processed: 234 average time/residue: 0.6678 time to fit residues: 172.5985 Evaluate side-chains 208 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 507 MET Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 188 GLU Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 384 VAL Chi-restraints excluded: chain J residue 440 VAL Chi-restraints excluded: chain J residue 507 MET Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 56 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.110100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075587 restraints weight = 34146.247| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.62 r_work: 0.2964 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18240 Z= 0.129 Angle : 0.527 7.312 24828 Z= 0.274 Chirality : 0.043 0.144 2780 Planarity : 0.005 0.075 3272 Dihedral : 4.028 16.983 2524 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.51 % Allowed : 21.19 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.18), residues: 2268 helix: 1.82 (0.19), residues: 776 sheet: 0.56 (0.22), residues: 556 loop : -0.14 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 593 TYR 0.011 0.001 TYR D 472 PHE 0.007 0.001 PHE D 577 TRP 0.011 0.002 TRP A 519 HIS 0.002 0.000 HIS G 586 Details of bonding type rmsd covalent geometry : bond 0.00302 (18240) covalent geometry : angle 0.52672 (24828) hydrogen bonds : bond 0.04661 ( 772) hydrogen bonds : angle 4.61050 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 0.679 Fit side-chains REVERT: A 354 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7689 (tpt) REVERT: A 403 GLN cc_start: 0.8668 (mt0) cc_final: 0.8125 (tp-100) REVERT: A 521 ASP cc_start: 0.8687 (m-30) cc_final: 0.8230 (m-30) REVERT: A 570 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: D 354 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7725 (tpt) REVERT: D 403 GLN cc_start: 0.8698 (mt0) cc_final: 0.8116 (tp-100) REVERT: D 521 ASP cc_start: 0.8644 (m-30) cc_final: 0.8191 (m-30) REVERT: G 354 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7725 (tpt) REVERT: G 403 GLN cc_start: 0.8682 (mt0) cc_final: 0.8098 (tp-100) REVERT: G 521 ASP cc_start: 0.8675 (m-30) cc_final: 0.8229 (m-30) REVERT: G 570 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: G 574 ASP cc_start: 0.8328 (m-30) cc_final: 0.8123 (m-30) REVERT: J 354 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7714 (tpt) REVERT: J 403 GLN cc_start: 0.8664 (mt0) cc_final: 0.8126 (tp-100) REVERT: J 521 ASP cc_start: 0.8564 (m-30) cc_final: 0.8184 (m-30) REVERT: J 574 ASP cc_start: 0.8335 (m-30) cc_final: 0.8123 (m-30) REVERT: K 593 ARG cc_start: 0.7620 (mtp-110) cc_final: 0.7075 (mtm110) outliers start: 48 outliers final: 7 residues processed: 223 average time/residue: 0.6349 time to fit residues: 157.3864 Evaluate side-chains 194 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 393 GLN Chi-restraints excluded: chain J residue 548 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 223 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 54 optimal weight: 0.0060 chunk 112 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074736 restraints weight = 34138.463| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.60 r_work: 0.2946 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18240 Z= 0.174 Angle : 0.558 9.723 24828 Z= 0.287 Chirality : 0.044 0.150 2780 Planarity : 0.005 0.072 3272 Dihedral : 3.997 16.356 2524 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.30 % Allowed : 21.24 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.18), residues: 2268 helix: 1.81 (0.19), residues: 776 sheet: 0.53 (0.22), residues: 556 loop : -0.11 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 593 TYR 0.011 0.001 TYR J 317 PHE 0.007 0.001 PHE D 88 TRP 0.009 0.002 TRP G 519 HIS 0.008 0.001 HIS J 140 Details of bonding type rmsd covalent geometry : bond 0.00426 (18240) covalent geometry : angle 0.55793 (24828) hydrogen bonds : bond 0.05200 ( 772) hydrogen bonds : angle 4.62108 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7605 (tpt) REVERT: A 403 GLN cc_start: 0.8670 (mt0) cc_final: 0.8333 (tm-30) REVERT: A 521 ASP cc_start: 0.8698 (m-30) cc_final: 0.8239 (m-30) REVERT: A 570 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: B 593 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7307 (mtm110) REVERT: D 354 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7657 (tpt) REVERT: D 403 GLN cc_start: 0.8703 (mt0) cc_final: 0.8169 (tp-100) REVERT: D 521 ASP cc_start: 0.8655 (m-30) cc_final: 0.8249 (m-30) REVERT: D 570 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: G 354 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7621 (tpt) REVERT: G 403 GLN cc_start: 0.8660 (mt0) cc_final: 0.8124 (tp-100) REVERT: G 521 ASP cc_start: 0.8688 (m-30) cc_final: 0.8236 (m-30) REVERT: G 570 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: G 574 ASP cc_start: 0.8355 (m-30) cc_final: 0.8150 (m-30) REVERT: H 593 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.7263 (mtm110) REVERT: J 354 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7598 (tpt) REVERT: J 403 GLN cc_start: 0.8672 (mt0) cc_final: 0.8332 (tm-30) REVERT: J 521 ASP cc_start: 0.8593 (m-30) cc_final: 0.8178 (m-30) REVERT: J 570 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: J 574 ASP cc_start: 0.8351 (m-30) cc_final: 0.8142 (m-30) REVERT: K 593 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7006 (mtm110) outliers start: 44 outliers final: 10 residues processed: 212 average time/residue: 0.6865 time to fit residues: 160.7637 Evaluate side-chains 197 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074857 restraints weight = 34419.294| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.62 r_work: 0.2950 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18240 Z= 0.179 Angle : 0.558 9.585 24828 Z= 0.287 Chirality : 0.044 0.149 2780 Planarity : 0.005 0.058 3272 Dihedral : 3.984 15.787 2524 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.41 % Allowed : 22.03 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.18), residues: 2268 helix: 1.85 (0.19), residues: 776 sheet: 0.48 (0.22), residues: 556 loop : -0.14 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 593 TYR 0.012 0.001 TYR D 472 PHE 0.008 0.001 PHE J 88 TRP 0.013 0.002 TRP J 519 HIS 0.001 0.000 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00437 (18240) covalent geometry : angle 0.55810 (24828) hydrogen bonds : bond 0.05122 ( 772) hydrogen bonds : angle 4.61778 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ASN cc_start: 0.8618 (m-40) cc_final: 0.8081 (t0) REVERT: A 354 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7564 (tpt) REVERT: A 403 GLN cc_start: 0.8687 (mt0) cc_final: 0.8325 (tm-30) REVERT: A 521 ASP cc_start: 0.8672 (m-30) cc_final: 0.8235 (m-30) REVERT: A 570 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: B 593 ARG cc_start: 0.7683 (mtp-110) cc_final: 0.7294 (mtm110) REVERT: D 351 ASN cc_start: 0.8620 (m-40) cc_final: 0.8076 (t0) REVERT: D 354 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7610 (tpt) REVERT: D 403 GLN cc_start: 0.8698 (mt0) cc_final: 0.8347 (tm-30) REVERT: D 521 ASP cc_start: 0.8643 (m-30) cc_final: 0.8243 (m-30) REVERT: D 570 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: G 351 ASN cc_start: 0.8616 (m-40) cc_final: 0.8078 (t0) REVERT: G 354 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7582 (tpt) REVERT: G 403 GLN cc_start: 0.8677 (mt0) cc_final: 0.8329 (tm-30) REVERT: G 521 ASP cc_start: 0.8642 (m-30) cc_final: 0.8254 (m-30) REVERT: G 570 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: G 574 ASP cc_start: 0.8362 (m-30) cc_final: 0.8154 (m-30) REVERT: J 351 ASN cc_start: 0.8617 (m-40) cc_final: 0.8072 (t0) REVERT: J 354 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7597 (tpt) REVERT: J 403 GLN cc_start: 0.8694 (mt0) cc_final: 0.8329 (tm-30) REVERT: J 521 ASP cc_start: 0.8601 (m-30) cc_final: 0.8228 (m-30) REVERT: J 570 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: J 574 ASP cc_start: 0.8364 (m-30) cc_final: 0.8156 (m-30) REVERT: K 593 ARG cc_start: 0.7599 (mtp-110) cc_final: 0.6980 (mtm110) outliers start: 27 outliers final: 4 residues processed: 200 average time/residue: 0.6721 time to fit residues: 148.3555 Evaluate side-chains 198 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 204 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 13 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 chunk 216 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076303 restraints weight = 34001.514| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.62 r_work: 0.2980 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18240 Z= 0.114 Angle : 0.517 9.277 24828 Z= 0.263 Chirality : 0.043 0.140 2780 Planarity : 0.005 0.049 3272 Dihedral : 3.746 14.773 2524 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.36 % Allowed : 22.18 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.18), residues: 2268 helix: 2.09 (0.20), residues: 776 sheet: 0.52 (0.22), residues: 556 loop : -0.15 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 593 TYR 0.009 0.001 TYR A 472 PHE 0.006 0.001 PHE A 577 TRP 0.010 0.001 TRP J 519 HIS 0.006 0.000 HIS J 140 Details of bonding type rmsd covalent geometry : bond 0.00272 (18240) covalent geometry : angle 0.51729 (24828) hydrogen bonds : bond 0.04077 ( 772) hydrogen bonds : angle 4.41045 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8086 (mpp80) cc_final: 0.7788 (mpp80) REVERT: A 351 ASN cc_start: 0.8552 (m-40) cc_final: 0.8024 (t0) REVERT: A 403 GLN cc_start: 0.8731 (mt0) cc_final: 0.8352 (tm-30) REVERT: A 521 ASP cc_start: 0.8584 (m-30) cc_final: 0.8181 (m-30) REVERT: A 570 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: B 593 ARG cc_start: 0.7505 (mtp-110) cc_final: 0.7198 (mtm110) REVERT: D 51 ARG cc_start: 0.8090 (mpp80) cc_final: 0.7785 (mpp80) REVERT: D 351 ASN cc_start: 0.8551 (m-40) cc_final: 0.8020 (t0) REVERT: D 403 GLN cc_start: 0.8694 (mt0) cc_final: 0.8316 (tm-30) REVERT: D 521 ASP cc_start: 0.8622 (m-30) cc_final: 0.8238 (m-30) REVERT: D 570 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: G 51 ARG cc_start: 0.8066 (mpp80) cc_final: 0.7766 (mpp80) REVERT: G 351 ASN cc_start: 0.8546 (m-40) cc_final: 0.8022 (t0) REVERT: G 521 ASP cc_start: 0.8589 (m-30) cc_final: 0.8206 (m-30) REVERT: G 570 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: G 574 ASP cc_start: 0.8335 (m-30) cc_final: 0.8124 (m-30) REVERT: H 593 ARG cc_start: 0.7725 (mtp-110) cc_final: 0.7336 (mtm180) REVERT: J 51 ARG cc_start: 0.8072 (mpp80) cc_final: 0.7774 (mpp80) REVERT: J 351 ASN cc_start: 0.8550 (m-40) cc_final: 0.8016 (t0) REVERT: J 403 GLN cc_start: 0.8702 (mt0) cc_final: 0.8340 (tm-30) REVERT: J 521 ASP cc_start: 0.8540 (m-30) cc_final: 0.8180 (m-30) REVERT: J 570 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: J 574 ASP cc_start: 0.8344 (m-30) cc_final: 0.8131 (m-30) REVERT: K 593 ARG cc_start: 0.7499 (mtp-110) cc_final: 0.6963 (mtm110) outliers start: 26 outliers final: 12 residues processed: 203 average time/residue: 0.6646 time to fit residues: 149.5011 Evaluate side-chains 199 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 75 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 222 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.109483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.075378 restraints weight = 34107.040| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.58 r_work: 0.2952 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18240 Z= 0.160 Angle : 0.543 9.635 24828 Z= 0.277 Chirality : 0.044 0.146 2780 Planarity : 0.005 0.076 3272 Dihedral : 3.835 14.713 2524 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.20 % Allowed : 21.97 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2268 helix: 1.95 (0.20), residues: 780 sheet: 0.52 (0.22), residues: 556 loop : -0.13 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 593 TYR 0.010 0.001 TYR D 472 PHE 0.007 0.001 PHE J 88 TRP 0.009 0.002 TRP J 519 HIS 0.002 0.000 HIS D 114 Details of bonding type rmsd covalent geometry : bond 0.00389 (18240) covalent geometry : angle 0.54344 (24828) hydrogen bonds : bond 0.04833 ( 772) hydrogen bonds : angle 4.48745 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ASN cc_start: 0.8603 (m-40) cc_final: 0.8056 (t0) REVERT: A 403 GLN cc_start: 0.8717 (mt0) cc_final: 0.8332 (tm-30) REVERT: A 521 ASP cc_start: 0.8618 (m-30) cc_final: 0.8279 (m-30) REVERT: A 570 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: D 351 ASN cc_start: 0.8600 (m-40) cc_final: 0.8048 (t0) REVERT: D 403 GLN cc_start: 0.8676 (mt0) cc_final: 0.8336 (tm-30) REVERT: D 521 ASP cc_start: 0.8644 (m-30) cc_final: 0.8210 (m-30) REVERT: D 570 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: G 351 ASN cc_start: 0.8604 (m-40) cc_final: 0.8054 (t0) REVERT: G 403 GLN cc_start: 0.8703 (mt0) cc_final: 0.8354 (tm-30) REVERT: G 521 ASP cc_start: 0.8600 (m-30) cc_final: 0.8209 (m-30) REVERT: G 570 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: G 574 ASP cc_start: 0.8353 (m-30) cc_final: 0.8149 (m-30) REVERT: H 593 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7248 (mtm180) REVERT: J 351 ASN cc_start: 0.8604 (m-40) cc_final: 0.8052 (t0) REVERT: J 403 GLN cc_start: 0.8726 (mt0) cc_final: 0.8298 (tm-30) REVERT: J 521 ASP cc_start: 0.8576 (m-30) cc_final: 0.8166 (m-30) REVERT: J 570 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: J 574 ASP cc_start: 0.8372 (m-30) cc_final: 0.8168 (m-30) REVERT: K 593 ARG cc_start: 0.7521 (mtp-110) cc_final: 0.6908 (mtm110) outliers start: 23 outliers final: 14 residues processed: 208 average time/residue: 0.6850 time to fit residues: 157.5629 Evaluate side-chains 205 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain J residue 514 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 22 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 HIS ** J 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.109461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.075373 restraints weight = 33837.757| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.58 r_work: 0.2967 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18240 Z= 0.150 Angle : 0.549 10.170 24828 Z= 0.281 Chirality : 0.044 0.144 2780 Planarity : 0.006 0.110 3272 Dihedral : 3.853 14.600 2524 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.15 % Allowed : 21.92 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2268 helix: 1.90 (0.19), residues: 780 sheet: 0.50 (0.22), residues: 556 loop : -0.11 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 593 TYR 0.010 0.001 TYR D 472 PHE 0.006 0.001 PHE J 88 TRP 0.010 0.002 TRP J 519 HIS 0.004 0.001 HIS D 114 Details of bonding type rmsd covalent geometry : bond 0.00363 (18240) covalent geometry : angle 0.54881 (24828) hydrogen bonds : bond 0.04654 ( 772) hydrogen bonds : angle 4.49637 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8087 (mpp80) cc_final: 0.7828 (mpp80) REVERT: A 351 ASN cc_start: 0.8608 (m-40) cc_final: 0.8064 (t0) REVERT: A 354 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7616 (tpt) REVERT: A 403 GLN cc_start: 0.8731 (mt0) cc_final: 0.8303 (tm-30) REVERT: A 521 ASP cc_start: 0.8669 (m-30) cc_final: 0.8194 (m-30) REVERT: A 570 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: B 593 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7369 (mtm180) REVERT: D 51 ARG cc_start: 0.8079 (mpp80) cc_final: 0.7821 (mpp80) REVERT: D 351 ASN cc_start: 0.8604 (m-40) cc_final: 0.8056 (t0) REVERT: D 354 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7640 (tpt) REVERT: D 403 GLN cc_start: 0.8707 (mt0) cc_final: 0.8342 (tm-30) REVERT: D 521 ASP cc_start: 0.8573 (m-30) cc_final: 0.8285 (p0) REVERT: D 570 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: G 51 ARG cc_start: 0.8069 (mpp80) cc_final: 0.7808 (mpp80) REVERT: G 351 ASN cc_start: 0.8606 (m-40) cc_final: 0.8061 (t0) REVERT: G 354 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7653 (tpt) REVERT: G 403 GLN cc_start: 0.8710 (mt0) cc_final: 0.8348 (tm-30) REVERT: G 521 ASP cc_start: 0.8560 (m-30) cc_final: 0.8192 (m-30) REVERT: G 570 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: G 574 ASP cc_start: 0.8351 (m-30) cc_final: 0.8146 (m-30) REVERT: H 593 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7174 (mtm180) REVERT: J 51 ARG cc_start: 0.8073 (mpp80) cc_final: 0.7815 (mpp80) REVERT: J 351 ASN cc_start: 0.8601 (m-40) cc_final: 0.8051 (t0) REVERT: J 354 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7650 (tpt) REVERT: J 403 GLN cc_start: 0.8738 (mt0) cc_final: 0.8280 (tm-30) REVERT: J 521 ASP cc_start: 0.8558 (m-30) cc_final: 0.8149 (m-30) REVERT: J 570 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: J 574 ASP cc_start: 0.8362 (m-30) cc_final: 0.8155 (m-30) REVERT: K 593 ARG cc_start: 0.7513 (mtp-110) cc_final: 0.6888 (mtm110) outliers start: 22 outliers final: 9 residues processed: 200 average time/residue: 0.6850 time to fit residues: 151.4304 Evaluate side-chains 201 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 548 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain G residue 354 MET Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 548 SER Chi-restraints excluded: chain G residue 570 GLU Chi-restraints excluded: chain J residue 354 MET Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 548 SER Chi-restraints excluded: chain J residue 570 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 98 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 82 optimal weight: 0.0470 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.110023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075752 restraints weight = 34243.211| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.61 r_work: 0.2973 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18240 Z= 0.126 Angle : 0.531 10.138 24828 Z= 0.270 Chirality : 0.043 0.141 2780 Planarity : 0.005 0.094 3272 Dihedral : 3.767 14.267 2524 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.25 % Allowed : 21.71 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2268 helix: 2.04 (0.19), residues: 780 sheet: 0.53 (0.22), residues: 556 loop : -0.14 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 593 TYR 0.009 0.001 TYR J 472 PHE 0.005 0.001 PHE D 577 TRP 0.010 0.002 TRP J 519 HIS 0.003 0.000 HIS J 114 Details of bonding type rmsd covalent geometry : bond 0.00303 (18240) covalent geometry : angle 0.53116 (24828) hydrogen bonds : bond 0.04275 ( 772) hydrogen bonds : angle 4.41161 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6009.95 seconds wall clock time: 102 minutes 39.76 seconds (6159.76 seconds total)