Starting phenix.real_space_refine on Sat Feb 7 20:31:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m3y_63611/02_2026/9m3y_63611.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m3y_63611/02_2026/9m3y_63611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m3y_63611/02_2026/9m3y_63611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m3y_63611/02_2026/9m3y_63611.map" model { file = "/net/cci-nas-00/data/ceres_data/9m3y_63611/02_2026/9m3y_63611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m3y_63611/02_2026/9m3y_63611.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 174 5.16 5 C 22272 2.51 5 N 6270 2.21 5 O 6954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35694 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5895 Classifications: {'peptide': 755} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 717} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 7.37, per 1000 atoms: 0.21 Number of scatterers: 35694 At special positions: 0 Unit cell: (179.3, 172.7, 101.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 174 16.00 P 24 15.00 O 6954 8.00 N 6270 7.00 C 22272 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: 3.32 Conformation dependent library (CDL) restraints added in 1.5 seconds 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8388 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 30 sheets defined 47.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.626A pdb=" N LYS A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 133 through 143 removed outlier: 4.767A pdb=" N LYS A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.730A pdb=" N VAL A 209 " --> pdb=" O TYR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 5.021A pdb=" N LEU A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.503A pdb=" N SER A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 Processing helix chain 'A' and resid 274 through 280 removed outlier: 3.593A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 removed outlier: 3.679A pdb=" N LEU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.589A pdb=" N THR A 319 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.502A pdb=" N ILE A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.731A pdb=" N ARG A 362 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.572A pdb=" N ILE A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 433 removed outlier: 4.033A pdb=" N VAL A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.588A pdb=" N PHE A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 485 through 502 removed outlier: 4.448A pdb=" N TYR A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 502 through 510 removed outlier: 4.087A pdb=" N PHE A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 559 through 571 removed outlier: 4.073A pdb=" N ARG A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.577A pdb=" N SER A 584 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 615 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 676 through 683 Processing helix chain 'A' and resid 687 through 720 removed outlier: 3.517A pdb=" N GLU A 712 " --> pdb=" O GLU A 708 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A 713 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 717 " --> pdb=" O LYS A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 752 through 764 removed outlier: 3.759A pdb=" N ILE A 756 " --> pdb=" O SER A 752 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 757 " --> pdb=" O ASP A 753 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 762 " --> pdb=" O LYS A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 removed outlier: 3.625A pdb=" N LYS B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 133 through 143 removed outlier: 4.766A pdb=" N LYS B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 205 through 209 removed outlier: 3.730A pdb=" N VAL B 209 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 removed outlier: 5.020A pdb=" N LEU B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Proline residue: B 226 - end of helix Processing helix chain 'B' and resid 231 through 237 removed outlier: 3.503A pdb=" N SER B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 274 through 280 removed outlier: 3.593A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 removed outlier: 3.679A pdb=" N LEU B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 319 removed outlier: 3.589A pdb=" N THR B 319 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.502A pdb=" N ILE B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.730A pdb=" N ARG B 362 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 388 Processing helix chain 'B' and resid 398 through 406 removed outlier: 3.572A pdb=" N ILE B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 433 removed outlier: 4.033A pdb=" N VAL B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 447 Processing helix chain 'B' and resid 451 through 462 removed outlier: 3.587A pdb=" N PHE B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 502 removed outlier: 4.449A pdb=" N TYR B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.087A pdb=" N PHE B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 507 " --> pdb=" O PRO B 503 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 538 Processing helix chain 'B' and resid 547 through 552 Processing helix chain 'B' and resid 559 through 571 removed outlier: 4.073A pdb=" N ARG B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.577A pdb=" N SER B 584 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 615 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 629 through 633 Processing helix chain 'B' and resid 653 through 665 Processing helix chain 'B' and resid 676 through 683 Processing helix chain 'B' and resid 687 through 720 removed outlier: 3.517A pdb=" N GLU B 712 " --> pdb=" O GLU B 708 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 713 " --> pdb=" O LYS B 709 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU B 714 " --> pdb=" O ASP B 710 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 752 through 764 removed outlier: 3.759A pdb=" N ILE B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 757 " --> pdb=" O ASP B 753 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 762 " --> pdb=" O LYS B 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 52 removed outlier: 3.626A pdb=" N LYS C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 133 through 143 removed outlier: 4.767A pdb=" N LYS C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.729A pdb=" N VAL C 209 " --> pdb=" O TYR C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 229 removed outlier: 5.021A pdb=" N LEU C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Proline residue: C 226 - end of helix Processing helix chain 'C' and resid 231 through 237 removed outlier: 3.503A pdb=" N SER C 235 " --> pdb=" O GLN C 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 Processing helix chain 'C' and resid 274 through 280 removed outlier: 3.593A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 299 removed outlier: 3.679A pdb=" N LEU C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 319 removed outlier: 3.588A pdb=" N THR C 319 " --> pdb=" O ARG C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 337 removed outlier: 3.502A pdb=" N ILE C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 329 " --> pdb=" O ARG C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.731A pdb=" N ARG C 362 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 388 Processing helix chain 'C' and resid 398 through 406 removed outlier: 3.573A pdb=" N ILE C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 433 removed outlier: 4.033A pdb=" N VAL C 432 " --> pdb=" O GLU C 428 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 433 " --> pdb=" O LYS C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 447 Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.587A pdb=" N PHE C 455 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'C' and resid 485 through 502 removed outlier: 4.448A pdb=" N TYR C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Proline residue: C 499 - end of helix Processing helix chain 'C' and resid 502 through 510 removed outlier: 4.087A pdb=" N PHE C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 507 " --> pdb=" O PRO C 503 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 509 " --> pdb=" O LYS C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 538 Processing helix chain 'C' and resid 547 through 552 Processing helix chain 'C' and resid 559 through 571 removed outlier: 4.073A pdb=" N ARG C 563 " --> pdb=" O GLU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 removed outlier: 3.577A pdb=" N SER C 584 " --> pdb=" O GLU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 615 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 629 through 633 Processing helix chain 'C' and resid 653 through 665 Processing helix chain 'C' and resid 676 through 683 Processing helix chain 'C' and resid 687 through 720 removed outlier: 3.518A pdb=" N GLU C 712 " --> pdb=" O GLU C 708 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS C 713 " --> pdb=" O LYS C 709 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU C 714 " --> pdb=" O ASP C 710 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 717 " --> pdb=" O LYS C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 745 through 747 No H-bonds generated for 'chain 'C' and resid 745 through 747' Processing helix chain 'C' and resid 752 through 764 removed outlier: 3.760A pdb=" N ILE C 756 " --> pdb=" O SER C 752 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 757 " --> pdb=" O ASP C 753 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 762 " --> pdb=" O LYS C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 removed outlier: 3.626A pdb=" N LYS D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 133 through 143 removed outlier: 4.768A pdb=" N LYS D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Proline residue: D 141 - end of helix Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.730A pdb=" N VAL D 209 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 229 removed outlier: 5.020A pdb=" N LEU D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Proline residue: D 226 - end of helix Processing helix chain 'D' and resid 231 through 237 removed outlier: 3.503A pdb=" N SER D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 Processing helix chain 'D' and resid 274 through 280 removed outlier: 3.593A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 299 removed outlier: 3.679A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 319 removed outlier: 3.589A pdb=" N THR D 319 " --> pdb=" O ARG D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.502A pdb=" N ILE D 327 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL D 328 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 removed outlier: 3.731A pdb=" N ARG D 362 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 388 Processing helix chain 'D' and resid 398 through 406 removed outlier: 3.572A pdb=" N ILE D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 433 removed outlier: 4.033A pdb=" N VAL D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 433 " --> pdb=" O LYS D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 447 Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.588A pdb=" N PHE D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 502 removed outlier: 4.449A pdb=" N TYR D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Proline residue: D 499 - end of helix Processing helix chain 'D' and resid 502 through 510 removed outlier: 4.087A pdb=" N PHE D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 507 " --> pdb=" O PRO D 503 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS D 508 " --> pdb=" O GLU D 504 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE D 509 " --> pdb=" O LYS D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 538 Processing helix chain 'D' and resid 547 through 552 Processing helix chain 'D' and resid 559 through 571 removed outlier: 4.073A pdb=" N ARG D 563 " --> pdb=" O GLU D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 removed outlier: 3.577A pdb=" N SER D 584 " --> pdb=" O GLU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 615 Processing helix chain 'D' and resid 616 through 618 No H-bonds generated for 'chain 'D' and resid 616 through 618' Processing helix chain 'D' and resid 629 through 633 Processing helix chain 'D' and resid 653 through 665 Processing helix chain 'D' and resid 676 through 683 Processing helix chain 'D' and resid 687 through 720 removed outlier: 3.517A pdb=" N GLU D 712 " --> pdb=" O GLU D 708 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 713 " --> pdb=" O LYS D 709 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU D 714 " --> pdb=" O ASP D 710 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 717 " --> pdb=" O LYS D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 744 Processing helix chain 'D' and resid 745 through 747 No H-bonds generated for 'chain 'D' and resid 745 through 747' Processing helix chain 'D' and resid 752 through 764 removed outlier: 3.759A pdb=" N ILE D 756 " --> pdb=" O SER D 752 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 757 " --> pdb=" O ASP D 753 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 762 " --> pdb=" O LYS D 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 52 removed outlier: 3.625A pdb=" N LYS E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 133 through 143 removed outlier: 4.767A pdb=" N LYS E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Proline residue: E 141 - end of helix Processing helix chain 'E' and resid 205 through 209 removed outlier: 3.730A pdb=" N VAL E 209 " --> pdb=" O TYR E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 229 removed outlier: 5.021A pdb=" N LEU E 225 " --> pdb=" O GLU E 221 " (cutoff:3.500A) Proline residue: E 226 - end of helix Processing helix chain 'E' and resid 231 through 237 removed outlier: 3.503A pdb=" N SER E 235 " --> pdb=" O GLN E 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 Processing helix chain 'E' and resid 274 through 280 removed outlier: 3.594A pdb=" N LYS E 280 " --> pdb=" O GLU E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 299 removed outlier: 3.680A pdb=" N LEU E 289 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 319 removed outlier: 3.589A pdb=" N THR E 319 " --> pdb=" O ARG E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 337 removed outlier: 3.502A pdb=" N ILE E 327 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL E 328 " --> pdb=" O GLU E 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 362 removed outlier: 3.730A pdb=" N ARG E 362 " --> pdb=" O ALA E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 388 Processing helix chain 'E' and resid 398 through 406 removed outlier: 3.572A pdb=" N ILE E 402 " --> pdb=" O ASP E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 433 removed outlier: 4.033A pdb=" N VAL E 432 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 433 " --> pdb=" O LYS E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 447 Processing helix chain 'E' and resid 451 through 462 removed outlier: 3.588A pdb=" N PHE E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 485 through 502 removed outlier: 4.448A pdb=" N TYR E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Proline residue: E 499 - end of helix Processing helix chain 'E' and resid 502 through 510 removed outlier: 4.087A pdb=" N PHE E 506 " --> pdb=" O HIS E 502 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 507 " --> pdb=" O PRO E 503 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS E 508 " --> pdb=" O GLU E 504 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE E 509 " --> pdb=" O LYS E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 538 Processing helix chain 'E' and resid 547 through 552 Processing helix chain 'E' and resid 559 through 571 removed outlier: 4.074A pdb=" N ARG E 563 " --> pdb=" O GLU E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.577A pdb=" N SER E 584 " --> pdb=" O GLU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 615 Processing helix chain 'E' and resid 616 through 618 No H-bonds generated for 'chain 'E' and resid 616 through 618' Processing helix chain 'E' and resid 629 through 633 Processing helix chain 'E' and resid 653 through 665 Processing helix chain 'E' and resid 676 through 683 Processing helix chain 'E' and resid 687 through 720 removed outlier: 3.517A pdb=" N GLU E 712 " --> pdb=" O GLU E 708 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 713 " --> pdb=" O LYS E 709 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU E 714 " --> pdb=" O ASP E 710 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 717 " --> pdb=" O LYS E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 744 Processing helix chain 'E' and resid 745 through 747 No H-bonds generated for 'chain 'E' and resid 745 through 747' Processing helix chain 'E' and resid 752 through 764 removed outlier: 3.759A pdb=" N ILE E 756 " --> pdb=" O SER E 752 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 757 " --> pdb=" O ASP E 753 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE E 762 " --> pdb=" O LYS E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 52 removed outlier: 3.626A pdb=" N LYS F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 133 through 143 removed outlier: 4.767A pdb=" N LYS F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Proline residue: F 141 - end of helix Processing helix chain 'F' and resid 205 through 209 removed outlier: 3.730A pdb=" N VAL F 209 " --> pdb=" O TYR F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 229 removed outlier: 5.021A pdb=" N LEU F 225 " --> pdb=" O GLU F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 231 through 237 removed outlier: 3.503A pdb=" N SER F 235 " --> pdb=" O GLN F 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY F 237 " --> pdb=" O PHE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 265 Processing helix chain 'F' and resid 274 through 280 removed outlier: 3.592A pdb=" N LYS F 280 " --> pdb=" O GLU F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 299 removed outlier: 3.679A pdb=" N LEU F 289 " --> pdb=" O SER F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 319 removed outlier: 3.589A pdb=" N THR F 319 " --> pdb=" O ARG F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.501A pdb=" N ILE F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 362 removed outlier: 3.732A pdb=" N ARG F 362 " --> pdb=" O ALA F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 388 Processing helix chain 'F' and resid 398 through 406 removed outlier: 3.572A pdb=" N ILE F 402 " --> pdb=" O ASP F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 433 removed outlier: 4.033A pdb=" N VAL F 432 " --> pdb=" O GLU F 428 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE F 433 " --> pdb=" O LYS F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 447 Processing helix chain 'F' and resid 451 through 462 removed outlier: 3.588A pdb=" N PHE F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 482 Processing helix chain 'F' and resid 485 through 502 removed outlier: 4.448A pdb=" N TYR F 498 " --> pdb=" O GLU F 494 " (cutoff:3.500A) Proline residue: F 499 - end of helix Processing helix chain 'F' and resid 502 through 510 removed outlier: 4.088A pdb=" N PHE F 506 " --> pdb=" O HIS F 502 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU F 507 " --> pdb=" O PRO F 503 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS F 508 " --> pdb=" O GLU F 504 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE F 509 " --> pdb=" O LYS F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 538 Processing helix chain 'F' and resid 547 through 552 Processing helix chain 'F' and resid 559 through 571 removed outlier: 4.074A pdb=" N ARG F 563 " --> pdb=" O GLU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.577A pdb=" N SER F 584 " --> pdb=" O GLU F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 615 Processing helix chain 'F' and resid 616 through 618 No H-bonds generated for 'chain 'F' and resid 616 through 618' Processing helix chain 'F' and resid 629 through 633 Processing helix chain 'F' and resid 653 through 665 Processing helix chain 'F' and resid 676 through 683 Processing helix chain 'F' and resid 687 through 720 removed outlier: 3.517A pdb=" N GLU F 712 " --> pdb=" O GLU F 708 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS F 713 " --> pdb=" O LYS F 709 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU F 714 " --> pdb=" O ASP F 710 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG F 717 " --> pdb=" O LYS F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 744 Processing helix chain 'F' and resid 745 through 747 No H-bonds generated for 'chain 'F' and resid 745 through 747' Processing helix chain 'F' and resid 752 through 764 removed outlier: 3.759A pdb=" N ILE F 756 " --> pdb=" O SER F 752 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 757 " --> pdb=" O ASP F 753 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE F 762 " --> pdb=" O LYS F 758 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 34 removed outlier: 8.275A pdb=" N ILE A 86 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 31 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET A 88 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP A 33 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 105 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 160 removed outlier: 6.579A pdb=" N HIS A 119 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR A 172 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG A 117 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 151 Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 273 removed outlier: 6.610A pdb=" N SER A 302 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N MET A 347 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 304 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA A 349 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE A 306 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 244 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR A 350 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 246 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY A 243 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 370 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 245 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 546 removed outlier: 6.543A pdb=" N ASN A 541 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE A 578 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 543 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP A 580 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 545 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A 516 " --> pdb=" O GLN A 645 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE A 647 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU A 518 " --> pdb=" O ILE A 647 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 34 removed outlier: 8.275A pdb=" N ILE B 86 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL B 31 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N MET B 88 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP B 33 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 105 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 155 through 160 removed outlier: 6.578A pdb=" N HIS B 119 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 172 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG B 117 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AA9, first strand: chain 'B' and resid 268 through 273 removed outlier: 6.610A pdb=" N SER B 302 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N MET B 347 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 304 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA B 349 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE B 306 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 244 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR B 350 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 246 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY B 243 " --> pdb=" O ARG B 368 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE B 370 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 245 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 541 through 546 removed outlier: 6.543A pdb=" N ASN B 541 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE B 578 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 543 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP B 580 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL B 545 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY B 516 " --> pdb=" O GLN B 645 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE B 647 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 518 " --> pdb=" O ILE B 647 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 34 removed outlier: 8.275A pdb=" N ILE C 86 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL C 31 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N MET C 88 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP C 33 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 105 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 155 through 160 removed outlier: 6.578A pdb=" N HIS C 119 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR C 172 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG C 117 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 149 through 151 Processing sheet with id=AB5, first strand: chain 'C' and resid 268 through 273 removed outlier: 6.611A pdb=" N SER C 302 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET C 347 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE C 304 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA C 349 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE C 306 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 244 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR C 350 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 246 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY C 243 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 370 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 245 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 541 through 546 removed outlier: 6.542A pdb=" N ASN C 541 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE C 578 " --> pdb=" O ASN C 541 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 543 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP C 580 " --> pdb=" O ILE C 543 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL C 545 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY C 516 " --> pdb=" O GLN C 645 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE C 647 " --> pdb=" O GLY C 516 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU C 518 " --> pdb=" O ILE C 647 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 34 removed outlier: 8.276A pdb=" N ILE D 86 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL D 31 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET D 88 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP D 33 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER D 105 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 160 removed outlier: 6.579A pdb=" N HIS D 119 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR D 172 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG D 117 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 149 through 151 Processing sheet with id=AC1, first strand: chain 'D' and resid 268 through 273 removed outlier: 6.610A pdb=" N SER D 302 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET D 347 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE D 304 " --> pdb=" O MET D 347 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA D 349 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE D 306 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE D 244 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR D 350 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU D 246 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY D 243 " --> pdb=" O ARG D 368 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE D 370 " --> pdb=" O GLY D 243 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU D 245 " --> pdb=" O ILE D 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 541 through 546 removed outlier: 6.543A pdb=" N ASN D 541 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE D 578 " --> pdb=" O ASN D 541 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE D 543 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP D 580 " --> pdb=" O ILE D 543 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL D 545 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY D 516 " --> pdb=" O GLN D 645 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE D 647 " --> pdb=" O GLY D 516 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU D 518 " --> pdb=" O ILE D 647 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 34 removed outlier: 8.276A pdb=" N ILE E 86 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL E 31 " --> pdb=" O ILE E 86 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET E 88 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP E 33 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER E 105 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 155 through 160 removed outlier: 6.579A pdb=" N HIS E 119 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR E 172 " --> pdb=" O ARG E 117 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG E 117 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 149 through 151 Processing sheet with id=AC6, first strand: chain 'E' and resid 268 through 273 removed outlier: 6.611A pdb=" N SER E 302 " --> pdb=" O ILE E 345 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N MET E 347 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE E 304 " --> pdb=" O MET E 347 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA E 349 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE E 306 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 244 " --> pdb=" O GLY E 348 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR E 350 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU E 246 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY E 243 " --> pdb=" O ARG E 368 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE E 370 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU E 245 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 541 through 546 removed outlier: 6.543A pdb=" N ASN E 541 " --> pdb=" O VAL E 576 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE E 578 " --> pdb=" O ASN E 541 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE E 543 " --> pdb=" O PHE E 578 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP E 580 " --> pdb=" O ILE E 543 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL E 545 " --> pdb=" O ASP E 580 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY E 516 " --> pdb=" O GLN E 645 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE E 647 " --> pdb=" O GLY E 516 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU E 518 " --> pdb=" O ILE E 647 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 29 through 34 removed outlier: 8.275A pdb=" N ILE F 86 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL F 31 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N MET F 88 " --> pdb=" O VAL F 31 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP F 33 " --> pdb=" O MET F 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 105 " --> pdb=" O LYS F 64 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 155 through 160 removed outlier: 6.578A pdb=" N HIS F 119 " --> pdb=" O ILE F 170 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR F 172 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG F 117 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 149 through 151 Processing sheet with id=AD2, first strand: chain 'F' and resid 268 through 273 removed outlier: 6.610A pdb=" N SER F 302 " --> pdb=" O ILE F 345 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET F 347 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE F 304 " --> pdb=" O MET F 347 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ALA F 349 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE F 306 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE F 244 " --> pdb=" O GLY F 348 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR F 350 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU F 246 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY F 243 " --> pdb=" O ARG F 368 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE F 370 " --> pdb=" O GLY F 243 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU F 245 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 541 through 546 removed outlier: 6.542A pdb=" N ASN F 541 " --> pdb=" O VAL F 576 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE F 578 " --> pdb=" O ASN F 541 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE F 543 " --> pdb=" O PHE F 578 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP F 580 " --> pdb=" O ILE F 543 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL F 545 " --> pdb=" O ASP F 580 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY F 516 " --> pdb=" O GLN F 645 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE F 647 " --> pdb=" O GLY F 516 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU F 518 " --> pdb=" O ILE F 647 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 4086 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: 9.58 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12231 1.34 - 1.46: 6643 1.46 - 1.58: 17120 1.58 - 1.70: 36 1.70 - 1.81: 270 Bond restraints: 36300 Sorted by residual: bond pdb=" C4 ADP E 901 " pdb=" C5 ADP E 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.21e+00 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.19e+00 ... (remaining 36295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 47811 1.31 - 2.62: 771 2.62 - 3.93: 287 3.93 - 5.23: 127 5.23 - 6.54: 36 Bond angle restraints: 49032 Sorted by residual: angle pdb=" N PHE B 762 " pdb=" CA PHE B 762 " pdb=" C PHE B 762 " ideal model delta sigma weight residual 113.43 109.09 4.34 1.26e+00 6.30e-01 1.19e+01 angle pdb=" N PHE C 762 " pdb=" CA PHE C 762 " pdb=" C PHE C 762 " ideal model delta sigma weight residual 113.43 109.09 4.34 1.26e+00 6.30e-01 1.18e+01 angle pdb=" N PHE E 762 " pdb=" CA PHE E 762 " pdb=" C PHE E 762 " ideal model delta sigma weight residual 113.43 109.09 4.34 1.26e+00 6.30e-01 1.18e+01 angle pdb=" N PHE A 762 " pdb=" CA PHE A 762 " pdb=" C PHE A 762 " ideal model delta sigma weight residual 113.43 109.10 4.33 1.26e+00 6.30e-01 1.18e+01 angle pdb=" N PHE D 762 " pdb=" CA PHE D 762 " pdb=" C PHE D 762 " ideal model delta sigma weight residual 113.43 109.10 4.33 1.26e+00 6.30e-01 1.18e+01 ... (remaining 49027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 21720 26.09 - 52.18: 618 52.18 - 78.27: 42 78.27 - 104.36: 0 104.36 - 130.45: 6 Dihedral angle restraints: 22386 sinusoidal: 9384 harmonic: 13002 Sorted by residual: dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 169.55 130.45 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP C 901 " pdb=" O3A ADP C 901 " pdb=" PB ADP C 901 " pdb=" PA ADP C 901 " ideal model delta sinusoidal sigma weight residual 300.00 169.56 130.44 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual 300.00 169.58 130.42 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 22383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3122 0.026 - 0.053: 1327 0.053 - 0.079: 454 0.079 - 0.105: 341 0.105 - 0.131: 186 Chirality restraints: 5430 Sorted by residual: chirality pdb=" CA ILE D 120 " pdb=" N ILE D 120 " pdb=" C ILE D 120 " pdb=" CB ILE D 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE C 120 " pdb=" N ILE C 120 " pdb=" C ILE C 120 " pdb=" CB ILE C 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 5427 not shown) Planarity restraints: 6474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 274 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO F 275 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 275 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 275 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 274 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO B 275 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 275 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 275 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 274 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO A 275 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " -0.019 5.00e-02 4.00e+02 ... (remaining 6471 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8854 2.80 - 3.33: 34337 3.33 - 3.85: 56883 3.85 - 4.38: 69162 4.38 - 4.90: 115099 Nonbonded interactions: 284335 Sorted by model distance: nonbonded pdb=" O GLY F 524 " pdb=" OG SER F 687 " model vdw 2.277 3.040 nonbonded pdb=" O GLY C 524 " pdb=" OG SER C 687 " model vdw 2.277 3.040 nonbonded pdb=" O GLY A 524 " pdb=" OG SER A 687 " model vdw 2.278 3.040 nonbonded pdb=" O GLY B 524 " pdb=" OG SER B 687 " model vdw 2.278 3.040 nonbonded pdb=" O GLY E 524 " pdb=" OG SER E 687 " model vdw 2.278 3.040 ... (remaining 284330 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.890 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 36300 Z= 0.107 Angle : 0.557 6.542 49032 Z= 0.290 Chirality : 0.042 0.131 5430 Planarity : 0.003 0.033 6474 Dihedral : 11.450 130.447 13998 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.59 % Favored : 96.15 % Rotamer: Outliers : 2.34 % Allowed : 6.25 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.75 (0.13), residues: 4518 helix: 0.88 (0.12), residues: 1998 sheet: 0.71 (0.19), residues: 750 loop : 0.14 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 341 TYR 0.008 0.001 TYR E 520 PHE 0.010 0.001 PHE C 156 TRP 0.003 0.001 TRP D 554 HIS 0.002 0.000 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00192 (36300) covalent geometry : angle 0.55690 (49032) hydrogen bonds : bond 0.15947 ( 1422) hydrogen bonds : angle 5.70316 ( 4086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 389 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.6829 (tpt) cc_final: 0.6585 (tpt) REVERT: A 371 ASP cc_start: 0.8461 (t0) cc_final: 0.8244 (t70) REVERT: B 371 ASP cc_start: 0.8316 (t0) cc_final: 0.8090 (t0) REVERT: C 50 MET cc_start: 0.6751 (mtm) cc_final: 0.6411 (mtm) REVERT: C 278 MET cc_start: 0.6713 (tpt) cc_final: 0.6447 (mmm) REVERT: C 316 ARG cc_start: 0.6325 (ttm-80) cc_final: 0.6116 (ttm-80) REVERT: C 615 MET cc_start: 0.8479 (tpp) cc_final: 0.8181 (tpt) REVERT: D 322 GLU cc_start: 0.5846 (tp30) cc_final: 0.5610 (tp30) REVERT: D 448 MET cc_start: 0.8454 (mtt) cc_final: 0.8238 (mtm) REVERT: D 468 ARG cc_start: 0.7956 (mpt90) cc_final: 0.7659 (mmt90) REVERT: E 177 TYR cc_start: 0.7601 (p90) cc_final: 0.7110 (p90) REVERT: F 88 MET cc_start: 0.6656 (mtm) cc_final: 0.6413 (mtm) REVERT: F 322 GLU cc_start: 0.5596 (tp30) cc_final: 0.5386 (tp30) REVERT: F 615 MET cc_start: 0.8432 (tpp) cc_final: 0.8166 (tpt) outliers start: 90 outliers final: 35 residues processed: 462 average time/residue: 0.7843 time to fit residues: 427.8098 Evaluate side-chains 266 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 746 TYR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 178 CYS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 746 TYR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 CYS Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 178 CYS Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 746 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.3980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 229 HIS A 288 ASN A 739 HIS A 764 GLN A 767 GLN B 218 GLN B 229 HIS B 288 ASN B 320 ASN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 764 GLN B 767 GLN C 218 GLN C 229 HIS C 288 ASN C 739 HIS C 764 GLN C 767 GLN D 218 GLN D 229 HIS D 288 ASN D 739 HIS D 764 GLN D 767 GLN E 218 GLN E 229 HIS E 288 ASN E 320 ASN ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 739 HIS E 764 GLN E 767 GLN F 218 GLN F 229 HIS F 288 ASN F 739 HIS F 764 GLN F 767 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.192131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152885 restraints weight = 43784.557| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.40 r_work: 0.3381 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 36300 Z= 0.217 Angle : 0.656 8.935 49032 Z= 0.322 Chirality : 0.048 0.191 5430 Planarity : 0.005 0.065 6474 Dihedral : 7.955 138.357 5099 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.41 % Favored : 96.33 % Rotamer: Outliers : 2.73 % Allowed : 9.51 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.49 (0.13), residues: 4518 helix: 0.64 (0.12), residues: 1980 sheet: 0.60 (0.19), residues: 672 loop : 0.06 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 748 TYR 0.018 0.002 TYR C 247 PHE 0.031 0.002 PHE D 762 TRP 0.008 0.002 TRP D 479 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00516 (36300) covalent geometry : angle 0.65650 (49032) hydrogen bonds : bond 0.05142 ( 1422) hydrogen bonds : angle 4.53618 ( 4086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 294 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.6957 (mtm) cc_final: 0.6663 (ttm) REVERT: A 74 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7069 (mt) REVERT: A 371 ASP cc_start: 0.8642 (t0) cc_final: 0.8372 (t70) REVERT: A 405 ASP cc_start: 0.6944 (t70) cc_final: 0.6585 (t70) REVERT: A 448 MET cc_start: 0.8709 (mtm) cc_final: 0.8473 (mtm) REVERT: A 467 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8448 (mm) REVERT: B 371 ASP cc_start: 0.8559 (t0) cc_final: 0.8344 (t0) REVERT: C 50 MET cc_start: 0.6774 (mtm) cc_final: 0.6524 (mtm) REVERT: C 456 HIS cc_start: 0.7273 (t70) cc_final: 0.7037 (t70) REVERT: C 693 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: D 448 MET cc_start: 0.8386 (mtt) cc_final: 0.8144 (mtm) REVERT: D 468 ARG cc_start: 0.7869 (mpt90) cc_final: 0.7540 (mmt90) REVERT: D 473 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7137 (pm20) REVERT: D 693 GLU cc_start: 0.7457 (pt0) cc_final: 0.6920 (tt0) REVERT: E 177 TYR cc_start: 0.7774 (p90) cc_final: 0.7046 (p90) REVERT: E 371 ASP cc_start: 0.8520 (t0) cc_final: 0.8295 (t0) REVERT: E 693 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7309 (pp20) REVERT: E 707 ILE cc_start: 0.7601 (mt) cc_final: 0.7365 (mm) REVERT: F 177 TYR cc_start: 0.7559 (p90) cc_final: 0.6779 (p90) REVERT: F 707 ILE cc_start: 0.7700 (mt) cc_final: 0.7496 (mm) outliers start: 105 outliers final: 57 residues processed: 372 average time/residue: 0.7442 time to fit residues: 331.3510 Evaluate side-chains 308 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 246 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 746 TYR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 746 TYR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 746 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 382 optimal weight: 2.9990 chunk 265 optimal weight: 0.4980 chunk 376 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 chunk 425 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 372 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.192329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153503 restraints weight = 43808.150| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.30 r_work: 0.3392 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 36300 Z= 0.164 Angle : 0.608 7.951 49032 Z= 0.292 Chirality : 0.046 0.178 5430 Planarity : 0.005 0.069 6474 Dihedral : 8.102 151.901 5088 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.30 % Favored : 96.44 % Rotamer: Outliers : 2.89 % Allowed : 11.07 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.36 (0.13), residues: 4518 helix: 0.58 (0.12), residues: 1980 sheet: 0.45 (0.20), residues: 630 loop : -0.03 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 748 TYR 0.018 0.001 TYR C 247 PHE 0.023 0.002 PHE F 762 TRP 0.005 0.001 TRP F 479 HIS 0.002 0.001 HIS F 46 Details of bonding type rmsd covalent geometry : bond 0.00387 (36300) covalent geometry : angle 0.60837 (49032) hydrogen bonds : bond 0.04444 ( 1422) hydrogen bonds : angle 4.31122 ( 4086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 254 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.6937 (mtm) cc_final: 0.6708 (ttm) REVERT: A 371 ASP cc_start: 0.8621 (t0) cc_final: 0.8399 (t70) REVERT: A 430 MET cc_start: 0.6618 (tmm) cc_final: 0.6120 (tpt) REVERT: A 448 MET cc_start: 0.8651 (mtm) cc_final: 0.8410 (mtm) REVERT: A 467 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8418 (mm) REVERT: B 177 TYR cc_start: 0.7762 (p90) cc_final: 0.7034 (p90) REVERT: C 50 MET cc_start: 0.6761 (mtm) cc_final: 0.6522 (mtm) REVERT: C 162 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8539 (mtt) REVERT: C 278 MET cc_start: 0.7239 (tpt) cc_final: 0.7007 (mmm) REVERT: C 456 HIS cc_start: 0.7291 (t70) cc_final: 0.7058 (t70) REVERT: C 686 PHE cc_start: 0.7824 (m-80) cc_final: 0.7615 (m-10) REVERT: C 707 ILE cc_start: 0.7753 (mt) cc_final: 0.7533 (mm) REVERT: D 448 MET cc_start: 0.8393 (mtt) cc_final: 0.8162 (mtm) REVERT: D 468 ARG cc_start: 0.7878 (mpt90) cc_final: 0.7661 (mtm-85) REVERT: D 473 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: D 563 ARG cc_start: 0.8711 (mtm110) cc_final: 0.8334 (mtp180) REVERT: D 629 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7221 (mtm-85) REVERT: D 693 GLU cc_start: 0.7346 (pt0) cc_final: 0.6862 (tt0) REVERT: E 177 TYR cc_start: 0.7808 (p90) cc_final: 0.7050 (p90) REVERT: E 371 ASP cc_start: 0.8514 (t0) cc_final: 0.8292 (t0) REVERT: E 693 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7237 (pp20) REVERT: E 707 ILE cc_start: 0.7718 (mt) cc_final: 0.7514 (mm) REVERT: F 128 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: F 177 TYR cc_start: 0.7525 (p90) cc_final: 0.6740 (p90) REVERT: F 430 MET cc_start: 0.6431 (mmm) cc_final: 0.5984 (tpt) outliers start: 111 outliers final: 64 residues processed: 340 average time/residue: 0.6935 time to fit residues: 283.8362 Evaluate side-chains 307 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 237 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 746 TYR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 696 GLN Chi-restraints excluded: chain D residue 746 TYR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 693 GLU Chi-restraints excluded: chain F residue 746 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 340 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 435 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 392 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 chunk 423 optimal weight: 0.0060 chunk 337 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS B 288 ASN C 107 HIS D 107 HIS E 288 ASN F 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.192731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154059 restraints weight = 43647.488| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.30 r_work: 0.3397 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36300 Z= 0.133 Angle : 0.577 10.405 49032 Z= 0.276 Chirality : 0.045 0.169 5430 Planarity : 0.004 0.060 6474 Dihedral : 8.164 166.766 5088 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.05 % Allowed : 12.66 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.48 (0.13), residues: 4518 helix: 0.70 (0.12), residues: 1980 sheet: 0.58 (0.20), residues: 642 loop : -0.02 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 748 TYR 0.015 0.001 TYR C 247 PHE 0.020 0.002 PHE B 762 TRP 0.005 0.001 TRP B 479 HIS 0.002 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00308 (36300) covalent geometry : angle 0.57682 (49032) hydrogen bonds : bond 0.03912 ( 1422) hydrogen bonds : angle 4.12062 ( 4086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 262 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6962 (mtm) cc_final: 0.6710 (ttm) REVERT: A 371 ASP cc_start: 0.8576 (t0) cc_final: 0.8302 (t70) REVERT: A 430 MET cc_start: 0.6692 (mmm) cc_final: 0.6152 (tpt) REVERT: A 448 MET cc_start: 0.8606 (mtm) cc_final: 0.8371 (mtm) REVERT: A 473 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: A 563 ARG cc_start: 0.8767 (mtm110) cc_final: 0.8384 (mtp180) REVERT: B 177 TYR cc_start: 0.7835 (p90) cc_final: 0.7072 (p90) REVERT: C 50 MET cc_start: 0.6777 (mtm) cc_final: 0.6566 (mtm) REVERT: C 162 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8529 (mtt) REVERT: C 177 TYR cc_start: 0.7657 (p90) cc_final: 0.6851 (p90) REVERT: C 213 ARG cc_start: 0.7543 (mmp80) cc_final: 0.7337 (mmp80) REVERT: C 278 MET cc_start: 0.7369 (tpt) cc_final: 0.7103 (mmm) REVERT: C 456 HIS cc_start: 0.7283 (t70) cc_final: 0.7051 (t70) REVERT: C 686 PHE cc_start: 0.7858 (m-80) cc_final: 0.7628 (m-10) REVERT: C 707 ILE cc_start: 0.7849 (mt) cc_final: 0.7631 (mm) REVERT: D 73 CYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7294 (p) REVERT: D 322 GLU cc_start: 0.5646 (tp30) cc_final: 0.5252 (tp30) REVERT: D 448 MET cc_start: 0.8395 (mtt) cc_final: 0.8174 (mtm) REVERT: D 468 ARG cc_start: 0.7850 (mpt90) cc_final: 0.7634 (mtm-85) REVERT: D 473 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: D 563 ARG cc_start: 0.8788 (mtm110) cc_final: 0.8429 (mtp180) REVERT: D 629 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7341 (mtm-85) REVERT: D 693 GLU cc_start: 0.7349 (pt0) cc_final: 0.6976 (pp20) REVERT: E 177 TYR cc_start: 0.7786 (p90) cc_final: 0.6994 (p90) REVERT: E 371 ASP cc_start: 0.8484 (t0) cc_final: 0.8279 (t0) REVERT: E 693 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: E 707 ILE cc_start: 0.7750 (mt) cc_final: 0.7536 (mm) REVERT: F 162 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8512 (mtt) REVERT: F 177 TYR cc_start: 0.7640 (p90) cc_final: 0.6893 (p90) REVERT: F 199 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: F 278 MET cc_start: 0.7304 (tpt) cc_final: 0.7065 (mmm) REVERT: F 430 MET cc_start: 0.6502 (mmm) cc_final: 0.6063 (tpt) outliers start: 117 outliers final: 76 residues processed: 357 average time/residue: 0.7163 time to fit residues: 307.9382 Evaluate side-chains 320 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 236 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 746 TYR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 746 TYR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 693 GLU Chi-restraints excluded: chain F residue 746 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 100 optimal weight: 0.0980 chunk 437 optimal weight: 2.9990 chunk 383 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 355 optimal weight: 0.0570 chunk 106 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 343 optimal weight: 6.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.193798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155573 restraints weight = 43658.821| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.27 r_work: 0.3423 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36300 Z= 0.107 Angle : 0.561 8.362 49032 Z= 0.266 Chirality : 0.044 0.160 5430 Planarity : 0.004 0.052 6474 Dihedral : 8.178 174.205 5088 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.99 % Favored : 96.75 % Rotamer: Outliers : 3.07 % Allowed : 13.36 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.64 (0.13), residues: 4518 helix: 0.84 (0.12), residues: 1974 sheet: 0.70 (0.20), residues: 642 loop : 0.05 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 213 TYR 0.012 0.001 TYR F 247 PHE 0.017 0.001 PHE E 740 TRP 0.005 0.001 TRP E 479 HIS 0.002 0.000 HIS D 456 Details of bonding type rmsd covalent geometry : bond 0.00240 (36300) covalent geometry : angle 0.56106 (49032) hydrogen bonds : bond 0.03481 ( 1422) hydrogen bonds : angle 4.00377 ( 4086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 257 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6926 (mtm) cc_final: 0.6689 (ttm) REVERT: A 177 TYR cc_start: 0.7683 (p90) cc_final: 0.6920 (p90) REVERT: A 371 ASP cc_start: 0.8570 (t0) cc_final: 0.8329 (t70) REVERT: A 430 MET cc_start: 0.6712 (mmm) cc_final: 0.6170 (tpt) REVERT: A 448 MET cc_start: 0.8587 (mtm) cc_final: 0.8337 (mtm) REVERT: A 467 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 473 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: A 563 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8478 (mtp85) REVERT: B 162 MET cc_start: 0.9112 (mtt) cc_final: 0.8888 (mpp) REVERT: B 177 TYR cc_start: 0.7668 (p90) cc_final: 0.6879 (p90) REVERT: C 50 MET cc_start: 0.6742 (mtm) cc_final: 0.6521 (mtm) REVERT: C 177 TYR cc_start: 0.7550 (p90) cc_final: 0.6875 (p90) REVERT: C 213 ARG cc_start: 0.7495 (mmp80) cc_final: 0.7276 (mmp80) REVERT: C 278 MET cc_start: 0.7326 (tpt) cc_final: 0.7107 (mmm) REVERT: C 456 HIS cc_start: 0.7215 (t70) cc_final: 0.7000 (t70) REVERT: C 473 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6956 (pt0) REVERT: C 707 ILE cc_start: 0.7836 (mt) cc_final: 0.7626 (mm) REVERT: D 73 CYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7359 (p) REVERT: D 177 TYR cc_start: 0.7617 (p90) cc_final: 0.6894 (p90) REVERT: D 322 GLU cc_start: 0.5569 (tp30) cc_final: 0.5211 (tp30) REVERT: D 448 MET cc_start: 0.8376 (mtt) cc_final: 0.8149 (mtm) REVERT: D 468 ARG cc_start: 0.7830 (mpt90) cc_final: 0.7611 (mtm-85) REVERT: D 473 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: D 563 ARG cc_start: 0.8759 (mtm110) cc_final: 0.8491 (mtp85) REVERT: D 693 GLU cc_start: 0.7450 (pt0) cc_final: 0.6964 (pp20) REVERT: E 177 TYR cc_start: 0.7669 (p90) cc_final: 0.6882 (p90) REVERT: E 371 ASP cc_start: 0.8466 (t0) cc_final: 0.8255 (t0) REVERT: E 693 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7376 (pp20) REVERT: F 128 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: F 177 TYR cc_start: 0.7659 (p90) cc_final: 0.6949 (p90) REVERT: F 430 MET cc_start: 0.6439 (mmm) cc_final: 0.6002 (tpt) REVERT: F 563 ARG cc_start: 0.8517 (mtm110) cc_final: 0.8273 (mtm-85) outliers start: 118 outliers final: 73 residues processed: 357 average time/residue: 0.7061 time to fit residues: 301.4265 Evaluate side-chains 321 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 746 TYR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 746 TYR Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 746 TYR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain E residue 746 TYR Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 693 GLU Chi-restraints excluded: chain F residue 746 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 376 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 391 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 440 optimal weight: 0.0020 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 696 GLN B 107 HIS B 288 ASN D 288 ASN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS E 288 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.192095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.153803 restraints weight = 43648.013| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.34 r_work: 0.3386 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36300 Z= 0.151 Angle : 0.598 10.658 49032 Z= 0.285 Chirality : 0.046 0.169 5430 Planarity : 0.004 0.062 6474 Dihedral : 8.403 179.544 5088 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.23 % Favored : 96.50 % Rotamer: Outliers : 3.26 % Allowed : 13.46 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.56 (0.13), residues: 4518 helix: 0.82 (0.12), residues: 1938 sheet: 0.51 (0.20), residues: 660 loop : 0.02 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 748 TYR 0.017 0.001 TYR C 247 PHE 0.017 0.002 PHE B 740 TRP 0.006 0.001 TRP B 479 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00358 (36300) covalent geometry : angle 0.59814 (49032) hydrogen bonds : bond 0.04016 ( 1422) hydrogen bonds : angle 4.03025 ( 4086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 260 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6942 (mtm) cc_final: 0.6699 (ttm) REVERT: A 177 TYR cc_start: 0.7755 (p90) cc_final: 0.6921 (p90) REVERT: A 371 ASP cc_start: 0.8607 (t0) cc_final: 0.8400 (t70) REVERT: A 430 MET cc_start: 0.6651 (mmm) cc_final: 0.6063 (tpt) REVERT: A 448 MET cc_start: 0.8596 (mtm) cc_final: 0.8356 (mtm) REVERT: A 467 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 473 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: A 563 ARG cc_start: 0.8736 (mtm110) cc_final: 0.8404 (mtp180) REVERT: A 748 ARG cc_start: 0.5675 (ttp80) cc_final: 0.5415 (ttp80) REVERT: B 162 MET cc_start: 0.9131 (mtt) cc_final: 0.8904 (mpp) REVERT: B 177 TYR cc_start: 0.7710 (p90) cc_final: 0.6889 (p90) REVERT: C 50 MET cc_start: 0.6807 (mtm) cc_final: 0.6582 (mtm) REVERT: C 177 TYR cc_start: 0.7661 (p90) cc_final: 0.6923 (p90) REVERT: C 213 ARG cc_start: 0.7556 (mmp80) cc_final: 0.7334 (mmp80) REVERT: C 278 MET cc_start: 0.7366 (tpt) cc_final: 0.7158 (mmm) REVERT: C 456 HIS cc_start: 0.7250 (t70) cc_final: 0.7045 (t70) REVERT: D 73 CYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7099 (p) REVERT: D 322 GLU cc_start: 0.5694 (tp30) cc_final: 0.5280 (tp30) REVERT: D 448 MET cc_start: 0.8449 (mtt) cc_final: 0.8223 (mtm) REVERT: D 473 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: D 563 ARG cc_start: 0.8784 (mtm110) cc_final: 0.8526 (mtp85) REVERT: D 693 GLU cc_start: 0.7418 (pt0) cc_final: 0.6915 (pp20) REVERT: E 177 TYR cc_start: 0.7700 (p90) cc_final: 0.6855 (p90) REVERT: E 371 ASP cc_start: 0.8534 (t0) cc_final: 0.8322 (t0) REVERT: E 693 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7269 (pp20) REVERT: F 128 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: F 177 TYR cc_start: 0.7744 (p90) cc_final: 0.7164 (p90) REVERT: F 199 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: F 430 MET cc_start: 0.6437 (mmm) cc_final: 0.6014 (tpt) REVERT: F 563 ARG cc_start: 0.8530 (mtm110) cc_final: 0.8288 (mtm-85) outliers start: 125 outliers final: 81 residues processed: 360 average time/residue: 0.6819 time to fit residues: 295.8357 Evaluate side-chains 327 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 239 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 696 GLN Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 693 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 401 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 436 optimal weight: 3.9990 chunk 279 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 175 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 354 optimal weight: 0.6980 chunk 254 optimal weight: 9.9990 chunk 444 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 696 GLN B 288 ASN B 354 ASN D 541 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.190448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151453 restraints weight = 43688.307| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.32 r_work: 0.3372 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 36300 Z= 0.198 Angle : 0.638 10.098 49032 Z= 0.308 Chirality : 0.047 0.178 5430 Planarity : 0.005 0.066 6474 Dihedral : 8.545 176.896 5076 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.22 % Rotamer: Outliers : 2.97 % Allowed : 14.09 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.35 (0.13), residues: 4518 helix: 0.67 (0.12), residues: 1914 sheet: 0.37 (0.20), residues: 660 loop : -0.11 (0.15), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 748 TYR 0.020 0.002 TYR F 247 PHE 0.020 0.002 PHE F 686 TRP 0.011 0.002 TRP F 554 HIS 0.003 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00473 (36300) covalent geometry : angle 0.63839 (49032) hydrogen bonds : bond 0.04520 ( 1422) hydrogen bonds : angle 4.14676 ( 4086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 252 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7030 (mtm) cc_final: 0.6777 (ttm) REVERT: A 177 TYR cc_start: 0.7624 (p90) cc_final: 0.6792 (p90) REVERT: A 371 ASP cc_start: 0.8626 (t0) cc_final: 0.8370 (t70) REVERT: A 405 ASP cc_start: 0.7010 (t70) cc_final: 0.6661 (t70) REVERT: A 430 MET cc_start: 0.6509 (mmm) cc_final: 0.6059 (tpt) REVERT: A 448 MET cc_start: 0.8630 (mtm) cc_final: 0.8395 (mtm) REVERT: A 467 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8341 (mm) REVERT: A 473 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: A 563 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8367 (mtp180) REVERT: A 658 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7861 (tp) REVERT: B 177 TYR cc_start: 0.7631 (p90) cc_final: 0.6812 (p90) REVERT: C 50 MET cc_start: 0.6850 (mtm) cc_final: 0.6629 (mtm) REVERT: C 177 TYR cc_start: 0.7671 (p90) cc_final: 0.6916 (p90) REVERT: C 278 MET cc_start: 0.7456 (tpt) cc_final: 0.7245 (mmm) REVERT: D 448 MET cc_start: 0.8446 (mtt) cc_final: 0.8214 (mtm) REVERT: D 473 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: D 563 ARG cc_start: 0.8737 (mtm110) cc_final: 0.8425 (mtp180) REVERT: D 693 GLU cc_start: 0.7426 (pt0) cc_final: 0.6904 (tt0) REVERT: E 177 TYR cc_start: 0.7634 (p90) cc_final: 0.6792 (p90) REVERT: E 371 ASP cc_start: 0.8562 (t0) cc_final: 0.8338 (t0) REVERT: E 693 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: F 177 TYR cc_start: 0.7646 (p90) cc_final: 0.7324 (p90) REVERT: F 199 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: F 430 MET cc_start: 0.6410 (mmm) cc_final: 0.5942 (tpt) outliers start: 114 outliers final: 81 residues processed: 348 average time/residue: 0.6518 time to fit residues: 275.3708 Evaluate side-chains 322 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 235 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 696 GLN Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 693 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 297 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 329 optimal weight: 7.9990 chunk 444 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 439 optimal weight: 0.0980 chunk 325 optimal weight: 0.4980 chunk 170 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN C 288 ASN D 424 GLN E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.192966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155225 restraints weight = 43643.898| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.22 r_work: 0.3418 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36300 Z= 0.110 Angle : 0.571 10.297 49032 Z= 0.274 Chirality : 0.045 0.166 5430 Planarity : 0.004 0.062 6474 Dihedral : 8.330 179.100 5076 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.66 % Rotamer: Outliers : 2.73 % Allowed : 14.56 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.55 (0.13), residues: 4518 helix: 0.84 (0.12), residues: 1938 sheet: 0.56 (0.21), residues: 648 loop : -0.06 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 748 TYR 0.012 0.001 TYR F 247 PHE 0.022 0.001 PHE C 135 TRP 0.006 0.001 TRP A 554 HIS 0.004 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00249 (36300) covalent geometry : angle 0.57100 (49032) hydrogen bonds : bond 0.03456 ( 1422) hydrogen bonds : angle 3.98720 ( 4086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 250 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.7592 (p90) cc_final: 0.6765 (p90) REVERT: A 371 ASP cc_start: 0.8569 (t0) cc_final: 0.8348 (t70) REVERT: A 430 MET cc_start: 0.6665 (mmm) cc_final: 0.6116 (tpt) REVERT: A 448 MET cc_start: 0.8606 (mtm) cc_final: 0.8383 (mtm) REVERT: A 473 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: A 563 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8463 (mtp85) REVERT: A 693 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: B 162 MET cc_start: 0.9121 (mtt) cc_final: 0.8897 (mpp) REVERT: B 177 TYR cc_start: 0.7586 (p90) cc_final: 0.6726 (p90) REVERT: C 50 MET cc_start: 0.6923 (mtm) cc_final: 0.6707 (mtm) REVERT: C 177 TYR cc_start: 0.7678 (p90) cc_final: 0.6896 (p90) REVERT: C 473 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7141 (pt0) REVERT: D 73 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7107 (p) REVERT: D 177 TYR cc_start: 0.7630 (p90) cc_final: 0.6931 (p90) REVERT: D 448 MET cc_start: 0.8424 (mtt) cc_final: 0.8199 (mtm) REVERT: D 473 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: D 563 ARG cc_start: 0.8756 (mtm110) cc_final: 0.8507 (mtp85) REVERT: E 177 TYR cc_start: 0.7587 (p90) cc_final: 0.6697 (p90) REVERT: E 371 ASP cc_start: 0.8467 (t0) cc_final: 0.8234 (t0) REVERT: E 453 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: E 693 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7234 (pp20) REVERT: F 177 TYR cc_start: 0.7603 (p90) cc_final: 0.7245 (p90) REVERT: F 430 MET cc_start: 0.6419 (mmm) cc_final: 0.5970 (tpt) REVERT: F 563 ARG cc_start: 0.8506 (mtm110) cc_final: 0.8271 (mtm-85) outliers start: 105 outliers final: 75 residues processed: 333 average time/residue: 0.6502 time to fit residues: 261.1199 Evaluate side-chains 315 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 233 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 693 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 17 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 402 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN B 288 ASN D 424 GLN E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.190819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.152925 restraints weight = 43619.039| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 3.28 r_work: 0.3374 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36300 Z= 0.171 Angle : 0.623 10.566 49032 Z= 0.300 Chirality : 0.047 0.169 5430 Planarity : 0.005 0.067 6474 Dihedral : 8.216 176.359 5076 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.50 % Favored : 96.37 % Rotamer: Outliers : 2.50 % Allowed : 15.03 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.37 (0.13), residues: 4518 helix: 0.69 (0.12), residues: 1938 sheet: 0.36 (0.20), residues: 666 loop : -0.11 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 748 TYR 0.019 0.001 TYR F 247 PHE 0.017 0.002 PHE A 363 TRP 0.011 0.002 TRP A 554 HIS 0.004 0.001 HIS E 456 Details of bonding type rmsd covalent geometry : bond 0.00406 (36300) covalent geometry : angle 0.62260 (49032) hydrogen bonds : bond 0.04218 ( 1422) hydrogen bonds : angle 4.07481 ( 4086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 239 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.7546 (p90) cc_final: 0.6710 (p90) REVERT: A 405 ASP cc_start: 0.7066 (t70) cc_final: 0.6735 (t70) REVERT: A 430 MET cc_start: 0.6510 (mmm) cc_final: 0.6016 (tpt) REVERT: A 448 MET cc_start: 0.8637 (mtm) cc_final: 0.8419 (mtm) REVERT: A 473 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7224 (pm20) REVERT: A 563 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8406 (mtp180) REVERT: B 162 MET cc_start: 0.9141 (mtt) cc_final: 0.8923 (mpp) REVERT: B 177 TYR cc_start: 0.7584 (p90) cc_final: 0.6755 (p90) REVERT: C 50 MET cc_start: 0.6922 (mtm) cc_final: 0.6706 (mtm) REVERT: C 177 TYR cc_start: 0.7624 (p90) cc_final: 0.6823 (p90) REVERT: D 177 TYR cc_start: 0.7595 (p90) cc_final: 0.6867 (p90) REVERT: D 448 MET cc_start: 0.8505 (mtt) cc_final: 0.8276 (mtm) REVERT: D 473 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: D 563 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8480 (mtp85) REVERT: D 693 GLU cc_start: 0.7332 (pt0) cc_final: 0.7072 (pp20) REVERT: E 177 TYR cc_start: 0.7604 (p90) cc_final: 0.6701 (p90) REVERT: E 371 ASP cc_start: 0.8567 (t0) cc_final: 0.8344 (t0) REVERT: E 563 ARG cc_start: 0.8652 (mtm110) cc_final: 0.8349 (mtm180) REVERT: E 693 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7278 (pp20) REVERT: F 177 TYR cc_start: 0.7555 (p90) cc_final: 0.7284 (p90) REVERT: F 430 MET cc_start: 0.6423 (mmm) cc_final: 0.6009 (tpt) REVERT: F 563 ARG cc_start: 0.8581 (mtm110) cc_final: 0.8336 (mtm-85) outliers start: 96 outliers final: 78 residues processed: 316 average time/residue: 0.6702 time to fit residues: 255.3293 Evaluate side-chains 315 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 234 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 696 GLN Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 693 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 125 optimal weight: 0.8980 chunk 366 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 310 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 406 optimal weight: 0.3980 chunk 320 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN C 107 HIS F 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.191418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.153370 restraints weight = 43793.846| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.26 r_work: 0.3393 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36300 Z= 0.144 Angle : 0.601 10.797 49032 Z= 0.290 Chirality : 0.046 0.166 5430 Planarity : 0.004 0.069 6474 Dihedral : 7.900 165.818 5076 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 2.37 % Allowed : 15.21 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.39 (0.13), residues: 4518 helix: 0.73 (0.12), residues: 1938 sheet: 0.37 (0.20), residues: 666 loop : -0.12 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 748 TYR 0.015 0.001 TYR F 247 PHE 0.027 0.002 PHE C 135 TRP 0.008 0.001 TRP A 554 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00341 (36300) covalent geometry : angle 0.60136 (49032) hydrogen bonds : bond 0.03879 ( 1422) hydrogen bonds : angle 4.05223 ( 4086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9036 Ramachandran restraints generated. 4518 Oldfield, 0 Emsley, 4518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 238 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 177 TYR cc_start: 0.7479 (p90) cc_final: 0.6568 (p90) REVERT: A 405 ASP cc_start: 0.7052 (t70) cc_final: 0.6742 (t70) REVERT: A 430 MET cc_start: 0.6521 (mmm) cc_final: 0.6047 (tpt) REVERT: A 448 MET cc_start: 0.8613 (mtm) cc_final: 0.8403 (mtm) REVERT: A 473 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: A 563 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8426 (mtp180) REVERT: A 744 MET cc_start: 0.7501 (mtp) cc_final: 0.7257 (ttm) REVERT: B 162 MET cc_start: 0.9140 (mtt) cc_final: 0.8920 (mpp) REVERT: B 177 TYR cc_start: 0.7557 (p90) cc_final: 0.6721 (p90) REVERT: C 50 MET cc_start: 0.6952 (mtm) cc_final: 0.6697 (mtm) REVERT: C 177 TYR cc_start: 0.7610 (p90) cc_final: 0.6814 (p90) REVERT: D 177 TYR cc_start: 0.7523 (p90) cc_final: 0.6828 (p90) REVERT: D 430 MET cc_start: 0.6283 (tmm) cc_final: 0.5960 (tpt) REVERT: D 448 MET cc_start: 0.8500 (mtt) cc_final: 0.8275 (mtm) REVERT: D 473 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: D 563 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8515 (mtp85) REVERT: D 693 GLU cc_start: 0.7343 (pt0) cc_final: 0.7098 (pp20) REVERT: E 177 TYR cc_start: 0.7539 (p90) cc_final: 0.6658 (p90) REVERT: E 371 ASP cc_start: 0.8545 (t0) cc_final: 0.8310 (t0) REVERT: E 693 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7237 (pp20) REVERT: F 177 TYR cc_start: 0.7513 (p90) cc_final: 0.7298 (p90) REVERT: F 430 MET cc_start: 0.6439 (mmm) cc_final: 0.6052 (tpt) outliers start: 91 outliers final: 79 residues processed: 313 average time/residue: 0.6315 time to fit residues: 239.7332 Evaluate side-chains 311 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 229 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 473 GLU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 620 THR Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 73 CYS Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 620 THR Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 696 GLN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 500 VAL Chi-restraints excluded: chain E residue 638 LEU Chi-restraints excluded: chain E residue 693 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 500 VAL Chi-restraints excluded: chain F residue 512 SER Chi-restraints excluded: chain F residue 620 THR Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 693 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 241 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 136 optimal weight: 0.0770 chunk 382 optimal weight: 0.0980 chunk 381 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 282 optimal weight: 0.0050 chunk 193 optimal weight: 1.9990 chunk 410 optimal weight: 0.6980 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN F 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.194360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.157318 restraints weight = 43731.466| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 3.17 r_work: 0.3437 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36300 Z= 0.098 Angle : 0.567 10.342 49032 Z= 0.272 Chirality : 0.044 0.162 5430 Planarity : 0.004 0.066 6474 Dihedral : 7.345 147.899 5076 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 2.11 % Allowed : 15.52 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.76 (0.13), residues: 4518 helix: 1.06 (0.12), residues: 1902 sheet: 0.61 (0.21), residues: 648 loop : 0.05 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 213 TYR 0.011 0.001 TYR F 247 PHE 0.016 0.001 PHE F 762 TRP 0.005 0.001 TRP B 479 HIS 0.004 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00213 (36300) covalent geometry : angle 0.56724 (49032) hydrogen bonds : bond 0.03080 ( 1422) hydrogen bonds : angle 3.90731 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10026.74 seconds wall clock time: 172 minutes 6.48 seconds (10326.48 seconds total)