Starting phenix.real_space_refine on Sun Aug 9 11:46:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/43ls_81969/08_2026/43ls_81969.cif Found real_map, /net/cci-nas-00/data/ceres_data/43ls_81969/08_2026/43ls_81969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/43ls_81969/08_2026/43ls_81969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/43ls_81969/08_2026/43ls_81969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/43ls_81969/08_2026/43ls_81969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/43ls_81969/08_2026/43ls_81969.map" } resolution = 1.36 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 20556 2.51 5 N 5748 2.21 5 O 7464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33920 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8126 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 56, 'TRANS': 946} Chain breaks: 1 Chain: "B" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8126 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 56, 'TRANS': 946} Chain breaks: 1 Chain: "C" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8126 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 56, 'TRANS': 946} Chain breaks: 1 Chain: "D" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8126 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 56, 'TRANS': 946} Chain breaks: 1 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 361 Classifications: {'water': 361} Link IDs: {None: 360} Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 359 Classifications: {'water': 359} Link IDs: {None: 358} Chain: "C" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 355 Classifications: {'water': 355} Link IDs: {None: 354} Chain: "D" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 341 Classifications: {'water': 341} Link IDs: {None: 340} Time building chain proxies: 6.47, per 1000 atoms: 0.19 Number of scatterers: 33920 At special positions: 0 Unit cell: (191.233, 100.858, 147.853, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 7464 8.00 N 5748 7.00 C 20556 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: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7520 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 56 sheets defined 17.2% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.621A pdb=" N ASN A 24 " --> pdb=" O ASP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.522A pdb=" N VAL A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.579A pdb=" N LEU A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.711A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.854A pdb=" N THR A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.644A pdb=" N ARG A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 485 removed outlier: 3.562A pdb=" N ASP A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.666A pdb=" N LEU A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 565 removed outlier: 3.979A pdb=" N TYR A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 removed outlier: 4.063A pdb=" N CYS A 608 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 removed outlier: 4.056A pdb=" N GLU A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 800 Processing helix chain 'A' and resid 811 through 820 Processing helix chain 'A' and resid 929 through 932 Processing helix chain 'A' and resid 969 through 976 Processing helix chain 'A' and resid 978 through 982 Processing helix chain 'A' and resid 1010 through 1014 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.644A pdb=" N ASN B 24 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.515A pdb=" N VAL B 75 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.578A pdb=" N LEU B 80 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 removed outlier: 3.695A pdb=" N LEU B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 402 through 412 removed outlier: 3.868A pdb=" N THR B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 removed outlier: 3.645A pdb=" N ARG B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 485 removed outlier: 3.607A pdb=" N ASP B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 removed outlier: 3.673A pdb=" N LEU B 530 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 565 removed outlier: 3.984A pdb=" N TYR B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 removed outlier: 4.002A pdb=" N CYS B 608 " --> pdb=" O ARG B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 removed outlier: 4.007A pdb=" N GLU B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 Processing helix chain 'B' and resid 811 through 820 Processing helix chain 'B' and resid 929 through 932 Processing helix chain 'B' and resid 969 through 976 Processing helix chain 'B' and resid 978 through 982 Processing helix chain 'B' and resid 1010 through 1014 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.649A pdb=" N ASN C 24 " --> pdb=" O ASP C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.525A pdb=" N VAL C 75 " --> pdb=" O PRO C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.573A pdb=" N LEU C 80 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 142 removed outlier: 3.691A pdb=" N LEU C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 374 through 388 Processing helix chain 'C' and resid 402 through 412 removed outlier: 3.868A pdb=" N THR C 406 " --> pdb=" O PRO C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 removed outlier: 3.645A pdb=" N ARG C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 485 removed outlier: 3.613A pdb=" N ASP C 475 " --> pdb=" O GLY C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 removed outlier: 3.702A pdb=" N LEU C 530 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER C 531 " --> pdb=" O LYS C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 565 removed outlier: 3.982A pdb=" N TYR C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 559 " --> pdb=" O PHE C 555 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 609 removed outlier: 4.038A pdb=" N CYS C 608 " --> pdb=" O ARG C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 630 removed outlier: 4.052A pdb=" N GLU C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 800 Processing helix chain 'C' and resid 811 through 820 Processing helix chain 'C' and resid 929 through 932 Processing helix chain 'C' and resid 969 through 976 Processing helix chain 'C' and resid 978 through 982 Processing helix chain 'C' and resid 1010 through 1014 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.641A pdb=" N ASN D 24 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.519A pdb=" N VAL D 75 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.577A pdb=" N LEU D 80 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 142 removed outlier: 3.697A pdb=" N LEU D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'D' and resid 402 through 412 removed outlier: 3.865A pdb=" N THR D 406 " --> pdb=" O PRO D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 454 removed outlier: 3.637A pdb=" N ARG D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 485 removed outlier: 3.613A pdb=" N ASP D 475 " --> pdb=" O GLY D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 531 removed outlier: 3.731A pdb=" N LEU D 530 " --> pdb=" O ILE D 526 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER D 531 " --> pdb=" O LYS D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 565 removed outlier: 3.985A pdb=" N TYR D 558 " --> pdb=" O GLY D 554 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 removed outlier: 4.038A pdb=" N CYS D 608 " --> pdb=" O ARG D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 removed outlier: 4.011A pdb=" N GLU D 625 " --> pdb=" O PRO D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 800 Processing helix chain 'D' and resid 811 through 820 Processing helix chain 'D' and resid 929 through 932 Processing helix chain 'D' and resid 969 through 976 Processing helix chain 'D' and resid 978 through 982 Processing helix chain 'D' and resid 1010 through 1014 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.738A pdb=" N LEU A 158 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR A 167 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE A 156 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY A 186 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 135 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 132 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLU A 63 " --> pdb=" O THR A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.534A pdb=" N ILE A 105 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 107 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 208 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 227 through 237 removed outlier: 5.449A pdb=" N ILE A 228 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N CYS A 253 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 279 removed outlier: 5.655A pdb=" N GLN A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN A 268 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 274 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR A 323 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU A 328 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 344 Processing sheet with id=AA8, first strand: chain 'A' and resid 490 through 491 removed outlier: 8.047A pdb=" N GLN A 491 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TRP A 462 " --> pdb=" O GLN A 491 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 415 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N SER A 463 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP A 417 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU A 418 " --> pdb=" O CYS A 395 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 539 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N PHE A 572 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 541 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 581 through 584 Processing sheet with id=AB1, first strand: chain 'A' and resid 633 through 638 Processing sheet with id=AB2, first strand: chain 'A' and resid 667 through 675 removed outlier: 6.733A pdb=" N VAL A 662 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A 671 " --> pdb=" O TRP A 660 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP A 660 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU A 673 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 658 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY A 698 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU A 730 " --> pdb=" O GLY A 698 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU A 700 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 722 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN A 708 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 720 " --> pdb=" O GLN A 708 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 745 through 748 removed outlier: 6.372A pdb=" N ASN A 765 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A 771 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.860A pdb=" N ILE A 888 " --> pdb=" O GLY A 994 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE A 995 " --> pdb=" O ASP A 960 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ASP A 960 " --> pdb=" O PHE A 995 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP A 960 " --> pdb=" O GLN A1023 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN A1023 " --> pdb=" O ASP A 960 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N GLN A 962 " --> pdb=" O HIS A1021 " (cutoff:3.500A) removed outlier: 13.279A pdb=" N HIS A1021 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 20.448A pdb=" N ASN A 964 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 23.322A pdb=" N ARG A1019 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N THR A 854 " --> pdb=" O HIS A 850 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS A 850 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA A 847 " --> pdb=" O LEU A 828 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 828 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLN A 849 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ALA A 826 " --> pdb=" O GLN A 849 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.860A pdb=" N ILE A 888 " --> pdb=" O GLY A 994 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE A 995 " --> pdb=" O ASP A 960 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ASP A 960 " --> pdb=" O PHE A 995 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG A 948 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A 961 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 946 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR A 947 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU A 906 " --> pdb=" O THR A 947 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.755A pdb=" N LEU B 158 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR B 167 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE B 156 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY B 186 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 135 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 132 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLU B 63 " --> pdb=" O THR B 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=AB8, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.542A pdb=" N ILE B 105 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 107 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET B 208 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AC1, first strand: chain 'B' and resid 227 through 237 removed outlier: 5.441A pdb=" N ILE B 228 " --> pdb=" O CYS B 253 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N CYS B 253 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 271 through 279 removed outlier: 5.657A pdb=" N GLN B 272 " --> pdb=" O GLN B 268 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN B 268 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 274 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 323 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU B 328 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 341 through 344 Processing sheet with id=AC4, first strand: chain 'B' and resid 490 through 491 removed outlier: 8.039A pdb=" N GLN B 491 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP B 462 " --> pdb=" O GLN B 491 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL B 415 " --> pdb=" O ILE B 460 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TRP B 462 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP B 417 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU B 418 " --> pdb=" O CYS B 395 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 539 " --> pdb=" O GLY B 570 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N PHE B 572 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 541 " --> pdb=" O PHE B 572 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 581 through 584 Processing sheet with id=AC6, first strand: chain 'B' and resid 633 through 638 Processing sheet with id=AC7, first strand: chain 'B' and resid 667 through 675 removed outlier: 6.738A pdb=" N VAL B 662 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER B 671 " --> pdb=" O TRP B 660 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP B 660 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 673 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 658 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY B 698 " --> pdb=" O GLU B 730 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU B 730 " --> pdb=" O GLY B 698 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU B 700 " --> pdb=" O LEU B 728 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 722 " --> pdb=" O VAL B 706 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN B 708 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 720 " --> pdb=" O GLN B 708 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 745 through 748 removed outlier: 6.359A pdb=" N ASN B 765 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 771 " --> pdb=" O ASN B 765 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 787 through 789 removed outlier: 6.860A pdb=" N ILE B 888 " --> pdb=" O GLY B 994 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 995 " --> pdb=" O ASP B 960 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N ASP B 960 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP B 960 " --> pdb=" O GLN B1023 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN B1023 " --> pdb=" O ASP B 960 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N GLN B 962 " --> pdb=" O HIS B1021 " (cutoff:3.500A) removed outlier: 13.270A pdb=" N HIS B1021 " --> pdb=" O GLN B 962 " (cutoff:3.500A) removed outlier: 20.434A pdb=" N ASN B 964 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 23.304A pdb=" N ARG B1019 " --> pdb=" O ASN B 964 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP B 848 " --> pdb=" O LEU B 855 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 857 " --> pdb=" O HIS B 846 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS B 846 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG B 859 " --> pdb=" O THR B 844 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR B 844 " --> pdb=" O ARG B 859 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR B 861 " --> pdb=" O ILE B 842 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE B 842 " --> pdb=" O THR B 861 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG B 863 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 840 " --> pdb=" O ARG B 863 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA B 847 " --> pdb=" O LEU B 828 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU B 828 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN B 849 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ALA B 826 " --> pdb=" O GLN B 849 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 787 through 789 removed outlier: 6.860A pdb=" N ILE B 888 " --> pdb=" O GLY B 994 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 995 " --> pdb=" O ASP B 960 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N ASP B 960 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 948 " --> pdb=" O GLY B 959 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE B 961 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 946 " --> pdb=" O PHE B 961 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR B 947 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 906 " --> pdb=" O THR B 947 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 29 through 30 removed outlier: 6.737A pdb=" N LEU C 158 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR C 167 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE C 156 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY C 186 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 135 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR C 132 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N GLU C 63 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 57 through 59 Processing sheet with id=AD4, first strand: chain 'C' and resid 105 through 107 removed outlier: 3.615A pdb=" N ILE C 105 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 107 " --> pdb=" O MET C 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET C 208 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AD6, first strand: chain 'C' and resid 227 through 237 removed outlier: 5.443A pdb=" N ILE C 228 " --> pdb=" O CYS C 253 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N CYS C 253 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 271 through 279 removed outlier: 5.658A pdb=" N GLN C 272 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN C 268 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 274 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR C 323 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 328 " --> pdb=" O THR C 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 341 through 344 Processing sheet with id=AD9, first strand: chain 'C' and resid 490 through 491 removed outlier: 8.055A pdb=" N GLN C 491 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TRP C 462 " --> pdb=" O GLN C 491 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL C 415 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TRP C 462 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP C 417 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU C 418 " --> pdb=" O CYS C 395 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 539 " --> pdb=" O GLY C 570 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N PHE C 572 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 541 " --> pdb=" O PHE C 572 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 581 through 584 Processing sheet with id=AE2, first strand: chain 'C' and resid 633 through 638 Processing sheet with id=AE3, first strand: chain 'C' and resid 667 through 675 removed outlier: 6.738A pdb=" N VAL C 662 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C 671 " --> pdb=" O TRP C 660 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP C 660 " --> pdb=" O SER C 671 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU C 673 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 658 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY C 698 " --> pdb=" O GLU C 730 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU C 730 " --> pdb=" O GLY C 698 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU C 700 " --> pdb=" O LEU C 728 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 722 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN C 708 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE C 720 " --> pdb=" O GLN C 708 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 745 through 748 removed outlier: 6.369A pdb=" N ASN C 765 " --> pdb=" O LEU C 771 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU C 771 " --> pdb=" O ASN C 765 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 787 through 789 removed outlier: 6.845A pdb=" N ILE C 888 " --> pdb=" O GLY C 994 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE C 995 " --> pdb=" O ASP C 960 " (cutoff:3.500A) removed outlier: 11.699A pdb=" N ASP C 960 " --> pdb=" O PHE C 995 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP C 960 " --> pdb=" O GLN C1023 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN C1023 " --> pdb=" O ASP C 960 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N GLN C 962 " --> pdb=" O HIS C1021 " (cutoff:3.500A) removed outlier: 13.233A pdb=" N HIS C1021 " --> pdb=" O GLN C 962 " (cutoff:3.500A) removed outlier: 20.422A pdb=" N ASN C 964 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 23.248A pdb=" N ARG C1019 " --> pdb=" O ASN C 964 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR C 854 " --> pdb=" O HIS C 850 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS C 850 " --> pdb=" O THR C 854 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA C 847 " --> pdb=" O LEU C 828 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU C 828 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN C 849 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA C 826 " --> pdb=" O GLN C 849 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 787 through 789 removed outlier: 6.845A pdb=" N ILE C 888 " --> pdb=" O GLY C 994 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE C 995 " --> pdb=" O ASP C 960 " (cutoff:3.500A) removed outlier: 11.699A pdb=" N ASP C 960 " --> pdb=" O PHE C 995 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG C 948 " --> pdb=" O GLY C 959 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE C 961 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 946 " --> pdb=" O PHE C 961 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR C 947 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU C 906 " --> pdb=" O THR C 947 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 29 through 30 removed outlier: 6.728A pdb=" N LEU D 158 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR D 167 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE D 156 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY D 186 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 135 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR D 132 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLU D 63 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 57 through 59 Processing sheet with id=AE9, first strand: chain 'D' and resid 105 through 107 removed outlier: 3.625A pdb=" N ILE D 105 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR D 107 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET D 208 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AF2, first strand: chain 'D' and resid 227 through 237 removed outlier: 5.392A pdb=" N ILE D 228 " --> pdb=" O CYS D 253 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N CYS D 253 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 271 through 279 removed outlier: 5.657A pdb=" N GLN D 272 " --> pdb=" O GLN D 268 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN D 268 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 274 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR D 323 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU D 328 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 341 through 344 Processing sheet with id=AF5, first strand: chain 'D' and resid 490 through 491 removed outlier: 8.034A pdb=" N GLN D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TRP D 462 " --> pdb=" O GLN D 491 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL D 415 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TRP D 462 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP D 417 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU D 418 " --> pdb=" O CYS D 395 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU D 539 " --> pdb=" O GLY D 570 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N PHE D 572 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU D 541 " --> pdb=" O PHE D 572 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 581 through 584 Processing sheet with id=AF7, first strand: chain 'D' and resid 633 through 638 Processing sheet with id=AF8, first strand: chain 'D' and resid 667 through 675 removed outlier: 6.737A pdb=" N VAL D 662 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER D 671 " --> pdb=" O TRP D 660 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP D 660 " --> pdb=" O SER D 671 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU D 673 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 658 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY D 698 " --> pdb=" O GLU D 730 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU D 730 " --> pdb=" O GLY D 698 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU D 700 " --> pdb=" O LEU D 728 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 722 " --> pdb=" O VAL D 706 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN D 708 " --> pdb=" O ILE D 720 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE D 720 " --> pdb=" O GLN D 708 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 745 through 748 removed outlier: 6.376A pdb=" N ASN D 765 " --> pdb=" O LEU D 771 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU D 771 " --> pdb=" O ASN D 765 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 787 through 789 removed outlier: 6.847A pdb=" N ILE D 888 " --> pdb=" O GLY D 994 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE D 995 " --> pdb=" O ASP D 960 " (cutoff:3.500A) removed outlier: 11.697A pdb=" N ASP D 960 " --> pdb=" O PHE D 995 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP D 960 " --> pdb=" O GLN D1023 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN D1023 " --> pdb=" O ASP D 960 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N GLN D 962 " --> pdb=" O HIS D1021 " (cutoff:3.500A) removed outlier: 13.251A pdb=" N HIS D1021 " --> pdb=" O GLN D 962 " (cutoff:3.500A) removed outlier: 20.424A pdb=" N ASN D 964 " --> pdb=" O ARG D1019 " (cutoff:3.500A) removed outlier: 23.249A pdb=" N ARG D1019 " --> pdb=" O ASN D 964 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR D 854 " --> pdb=" O HIS D 850 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS D 850 " --> pdb=" O THR D 854 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA D 847 " --> pdb=" O LEU D 828 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU D 828 " --> pdb=" O ALA D 847 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN D 849 " --> pdb=" O ALA D 826 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ALA D 826 " --> pdb=" O GLN D 849 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 787 through 789 removed outlier: 6.847A pdb=" N ILE D 888 " --> pdb=" O GLY D 994 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE D 995 " --> pdb=" O ASP D 960 " (cutoff:3.500A) removed outlier: 11.697A pdb=" N ASP D 960 " --> pdb=" O PHE D 995 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG D 948 " --> pdb=" O GLY D 959 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE D 961 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 946 " --> pdb=" O PHE D 961 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR D 947 " --> pdb=" O LEU D 906 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 906 " --> pdb=" O THR D 947 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3300 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: 8.78 Time building geometry restraints manager: 3.57 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: 10868 1.34 - 1.46: 8333 1.46 - 1.58: 14019 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 33460 Sorted by residual: bond pdb=" C HIS D 36 " pdb=" N PRO D 37 " ideal model delta sigma weight residual 1.329 1.357 -0.027 1.18e-02 7.18e+03 5.38e+00 bond pdb=" C HIS B 36 " pdb=" N PRO B 37 " ideal model delta sigma weight residual 1.329 1.357 -0.027 1.18e-02 7.18e+03 5.36e+00 bond pdb=" C HIS C 36 " pdb=" N PRO C 37 " ideal model delta sigma weight residual 1.329 1.357 -0.027 1.18e-02 7.18e+03 5.36e+00 bond pdb=" C HIS A 36 " pdb=" N PRO A 37 " ideal model delta sigma weight residual 1.329 1.357 -0.027 1.18e-02 7.18e+03 5.36e+00 bond pdb=" C ASN C 116 " pdb=" N PRO C 117 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.18e-02 7.18e+03 5.25e+00 ... (remaining 33455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 36652 1.49 - 2.97: 7412 2.97 - 4.46: 1411 4.46 - 5.94: 154 5.94 - 7.43: 15 Bond angle restraints: 45644 Sorted by residual: angle pdb=" CA ASP C 575 " pdb=" CB ASP C 575 " pdb=" CG ASP C 575 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CA ASP A 575 " pdb=" CB ASP A 575 " pdb=" CG ASP A 575 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CA ASP A 409 " pdb=" CB ASP A 409 " pdb=" CG ASP A 409 " ideal model delta sigma weight residual 112.60 117.05 -4.45 1.00e+00 1.00e+00 1.98e+01 angle pdb=" CA ASP D 575 " pdb=" CB ASP D 575 " pdb=" CG ASP D 575 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" CA ASP B 575 " pdb=" CB ASP B 575 " pdb=" CG ASP B 575 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.00e+00 1.00e+00 1.96e+01 ... (remaining 45639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 18070 15.42 - 30.83: 1041 30.83 - 46.25: 204 46.25 - 61.66: 146 61.66 - 77.08: 123 Dihedral angle restraints: 19584 sinusoidal: 7904 harmonic: 11680 Sorted by residual: dihedral pdb=" CA PHE B 963 " pdb=" C PHE B 963 " pdb=" N ASN B 964 " pdb=" CA ASN B 964 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA PHE C 963 " pdb=" C PHE C 963 " pdb=" N ASN C 964 " pdb=" CA ASN C 964 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PHE D 963 " pdb=" C PHE D 963 " pdb=" N ASN D 964 " pdb=" CA ASN D 964 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 19581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2645 0.050 - 0.100: 1370 0.100 - 0.149: 403 0.149 - 0.199: 264 0.199 - 0.249: 86 Chirality restraints: 4768 Sorted by residual: chirality pdb=" CA ASP C 604 " pdb=" N ASP C 604 " pdb=" C ASP C 604 " pdb=" CB ASP C 604 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASP D 604 " pdb=" N ASP D 604 " pdb=" C ASP D 604 " pdb=" CB ASP D 604 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA PRO D 913 " pdb=" N PRO D 913 " pdb=" C PRO D 913 " pdb=" CB PRO D 913 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 4765 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 559 " 0.019 2.00e-02 2.50e+03 1.02e-02 2.60e+00 pdb=" CG TRP A 559 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 559 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 559 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 559 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 559 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 559 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 559 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 559 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 559 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 559 " -0.019 2.00e-02 2.50e+03 1.01e-02 2.54e+00 pdb=" CG TRP B 559 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP B 559 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 559 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 559 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 559 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 559 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 559 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 559 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 559 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 559 " -0.019 2.00e-02 2.50e+03 1.00e-02 2.52e+00 pdb=" CG TRP D 559 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP D 559 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 559 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D 559 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 559 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 559 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 559 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 559 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 559 " -0.011 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 12752 2.87 - 3.38: 31447 3.38 - 3.89: 69855 3.89 - 4.39: 80292 4.39 - 4.90: 129050 Nonbonded interactions: 323396 Sorted by model distance: nonbonded pdb=" O HOH D1356 " pdb=" O HOH D1400 " model vdw 2.366 3.040 nonbonded pdb=" NE2 GLN C 893 " pdb=" O GLU C 986 " model vdw 2.440 3.120 nonbonded pdb=" O LEU C 928 " pdb=" O HOH C1101 " model vdw 2.451 3.040 nonbonded pdb=" NE2 GLN B 893 " pdb=" O GLU B 986 " model vdw 2.452 3.120 nonbonded pdb=" OD1 ASP C 865 " pdb=" OG SER C 867 " model vdw 2.453 3.040 ... (remaining 323391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 39.510 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: 0.040 Extract box with map and model: 1.760 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.180 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.007 0.038 33460 Z= 0.441 Angle : 1.245 7.426 45644 Z= 0.851 Chirality : 0.076 0.249 4768 Planarity : 0.003 0.029 6024 Dihedral : 13.516 77.080 12064 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.55 % Allowed : 2.86 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.12), residues: 4028 helix: -2.14 (0.19), residues: 548 sheet: -0.25 (0.14), residues: 1232 loop : -1.28 (0.11), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 787 TYR 0.021 0.002 TYR A 106 PHE 0.013 0.001 PHE B 650 TRP 0.020 0.002 TRP A 559 HIS 0.006 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.44 (33460) covalent geometry : angle 1.24478 / 0.85 (45644) hydrogen bonds : bond 0.19656 / 12.98 ( 1201) hydrogen bonds : angle 8.75540 / 6.12 ( 3300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 579 time to evaluate : 0.940 Fit side-chains REVERT: A 242 SER cc_start: 0.7314 (p) cc_final: 0.7060 (p) REVERT: A 298 ARG cc_start: 0.5980 (mtt90) cc_final: 0.5778 (mtt-85) REVERT: B 242 SER cc_start: 0.7308 (p) cc_final: 0.7055 (p) outliers start: 19 outliers final: 0 residues processed: 595 average time/residue: 0.8033 time to fit residues: 552.6191 Evaluate side-chains 481 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 401 HIS A 579 GLN A 620 HIS A 710 ASN A 724 GLN A 781 GLN A 851 GLN A 891 ASN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 401 HIS B 620 HIS B 652 HIS B 710 ASN B 724 GLN B 781 GLN B 830 GLN B 851 GLN B 891 ASN B 893 GLN C 169 GLN C 401 HIS C 620 HIS C 652 HIS C 710 ASN C 781 GLN C 830 GLN C 851 GLN C 891 ASN C 893 GLN ** C1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 401 HIS D 579 GLN D 620 HIS D 652 HIS D 710 ASN D 767 GLN D 781 GLN D 830 GLN D 851 GLN D 891 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.187823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.158295 restraints weight = 10736.424| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 0.34 r_work: 0.3455 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.3253 rms_B_bonded: 2.46 restraints_weight: 0.1250 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33460 Z= 0.180 Angle : 0.679 8.033 45644 Z= 0.372 Chirality : 0.047 0.170 4768 Planarity : 0.005 0.044 6024 Dihedral : 5.725 21.194 4424 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.64 % Allowed : 3.67 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: -0.32 (0.13), residues: 4028 helix: -0.81 (0.20), residues: 548 sheet: 0.11 (0.14), residues: 1284 loop : -0.12 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 605 TYR 0.025 0.003 TYR C 106 PHE 0.018 0.002 PHE A 995 TRP 0.036 0.002 TRP B 559 HIS 0.009 0.002 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (33460) covalent geometry : angle 0.67881 / 0.37 (45644) hydrogen bonds : bond 0.06061 / 3.96 ( 1201) hydrogen bonds : angle 6.48166 / 4.50 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 497 time to evaluate : 1.310 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 4 residues processed: 514 average time/residue: 0.8601 time to fit residues: 508.1564 Evaluate side-chains 473 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 469 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 307 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 346 optimal weight: 6.9990 chunk 25 optimal weight: 0.2980 chunk 371 optimal weight: 3.9990 chunk 318 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 220 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 169 GLN A 652 HIS A 710 ASN A 823 GLN A 891 ASN B 18 GLN B 652 HIS B 710 ASN B 830 GLN B 891 ASN C 18 GLN C 652 HIS C 710 ASN C 724 GLN C 830 GLN C 891 ASN D 18 GLN D 169 GLN D 652 HIS D 710 ASN D 830 GLN D 891 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.190712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.162790 restraints weight = 10809.093| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 0.33 r_work: 0.3507 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 1.12 restraints_weight: 0.2500 r_work: 0.3321 rms_B_bonded: 2.24 restraints_weight: 0.1250 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 33460 Z= 0.127 Angle : 0.578 7.331 45644 Z= 0.314 Chirality : 0.045 0.152 4768 Planarity : 0.004 0.039 6024 Dihedral : 5.444 20.327 4424 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.49 % Allowed : 4.36 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 0.07 (0.13), residues: 4028 helix: -0.36 (0.21), residues: 548 sheet: 0.25 (0.14), residues: 1320 loop : 0.18 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 298 TYR 0.022 0.002 TYR A 106 PHE 0.012 0.001 PHE A 995 TRP 0.036 0.002 TRP D 559 HIS 0.004 0.001 HIS C 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (33460) covalent geometry : angle 0.57795 / 0.31 (45644) hydrogen bonds : bond 0.04784 / 3.14 ( 1201) hydrogen bonds : angle 6.09757 / 4.24 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 491 time to evaluate : 1.147 Fit side-chains REVERT: B 298 ARG cc_start: 0.6608 (mtt90) cc_final: 0.6407 (mtt-85) REVERT: B 975 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6668 (mt-10) REVERT: D 975 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6684 (mt-10) outliers start: 17 outliers final: 7 residues processed: 503 average time/residue: 0.8540 time to fit residues: 494.0714 Evaluate side-chains 484 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 477 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 962 GLN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 962 GLN Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 962 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 4 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 358 optimal weight: 0.3980 chunk 281 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 308 optimal weight: 4.9990 chunk 366 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 154 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 373 optimal weight: 0.1980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 620 HIS A 652 HIS A 710 ASN A 823 GLN A 891 ASN A 955 HIS B 18 GLN B 652 HIS B 710 ASN B 830 GLN B 891 ASN B 955 HIS ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN C 652 HIS C 710 ASN C 830 GLN C 891 ASN C 955 HIS D 18 GLN D 652 HIS D 710 ASN D 830 GLN D 891 ASN D 955 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.189500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.161599 restraints weight = 10679.816| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 0.34 r_work: 0.3483 rms_B_bonded: 0.85 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 1.09 restraints_weight: 0.2500 r_work: 0.3279 rms_B_bonded: 2.52 restraints_weight: 0.1250 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33460 Z= 0.137 Angle : 0.595 7.802 45644 Z= 0.322 Chirality : 0.045 0.147 4768 Planarity : 0.004 0.031 6024 Dihedral : 5.470 20.742 4424 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.81 % Allowed : 4.53 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 0.23 (0.13), residues: 4028 helix: -0.29 (0.21), residues: 548 sheet: 0.29 (0.14), residues: 1320 loop : 0.35 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 236 TYR 0.022 0.002 TYR A 106 PHE 0.012 0.001 PHE C 995 TRP 0.036 0.002 TRP D 559 HIS 0.004 0.001 HIS D 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (33460) covalent geometry : angle 0.59454 / 0.32 (45644) hydrogen bonds : bond 0.04816 / 3.16 ( 1201) hydrogen bonds : angle 6.03553 / 4.19 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 483 time to evaluate : 1.385 Fit side-chains REVERT: A 975 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6748 (mt-10) REVERT: B 975 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6752 (mt-10) REVERT: C 975 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6715 (mt-10) REVERT: D 975 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6757 (mt-10) outliers start: 28 outliers final: 11 residues processed: 505 average time/residue: 0.8935 time to fit residues: 519.5388 Evaluate side-chains 478 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 467 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 962 GLN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 962 GLN Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 962 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 353 optimal weight: 0.3980 chunk 385 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 381 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 HIS A 652 HIS A 710 ASN A 823 GLN A 891 ASN A 955 HIS ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 620 HIS B 652 HIS B 710 ASN B 830 GLN B 891 ASN B 955 HIS C 18 GLN C 620 HIS C 652 HIS C 710 ASN C 830 GLN C 891 ASN C 955 HIS ** C1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 620 HIS D 652 HIS D 710 ASN D 830 GLN D 891 ASN D 955 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.188129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.159911 restraints weight = 10715.444| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 0.34 r_work: 0.3466 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 1.09 restraints_weight: 0.2500 r_work: 0.3273 rms_B_bonded: 2.35 restraints_weight: 0.1250 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33460 Z= 0.153 Angle : 0.621 8.247 45644 Z= 0.337 Chirality : 0.046 0.150 4768 Planarity : 0.004 0.041 6024 Dihedral : 5.568 21.408 4424 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.61 % Allowed : 4.99 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 0.31 (0.13), residues: 4028 helix: -0.33 (0.21), residues: 548 sheet: 0.30 (0.14), residues: 1344 loop : 0.47 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 605 TYR 0.023 0.002 TYR C 106 PHE 0.014 0.002 PHE C 995 TRP 0.038 0.002 TRP D 559 HIS 0.004 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (33460) covalent geometry : angle 0.62090 / 0.34 (45644) hydrogen bonds : bond 0.05097 / 3.34 ( 1201) hydrogen bonds : angle 6.09645 / 4.23 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 487 time to evaluate : 1.456 Fit side-chains REVERT: B 975 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6714 (mt-10) REVERT: D 751 MET cc_start: 0.4623 (mmm) cc_final: 0.4362 (mmm) REVERT: D 975 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6725 (mt-10) outliers start: 21 outliers final: 7 residues processed: 503 average time/residue: 0.9937 time to fit residues: 574.4302 Evaluate side-chains 473 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 466 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 147 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 258 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 370 optimal weight: 3.9990 chunk 255 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 338 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 HIS A 652 HIS A 710 ASN A 823 GLN A 891 ASN A 955 HIS A1021 HIS B 18 GLN B 620 HIS B 652 HIS B 710 ASN B 823 GLN B 830 GLN B 891 ASN B 955 HIS B1021 HIS C 18 GLN C 620 HIS C 652 HIS C 710 ASN C 823 GLN C 830 GLN C 891 ASN C 955 HIS C1021 HIS D 18 GLN D 620 HIS D 652 HIS D 710 ASN D 830 GLN D 891 ASN D 955 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.185058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.157651 restraints weight = 10569.689| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 0.32 r_work: 0.3441 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.3233 rms_B_bonded: 2.25 restraints_weight: 0.1250 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33460 Z= 0.229 Angle : 0.738 9.309 45644 Z= 0.401 Chirality : 0.049 0.158 4768 Planarity : 0.006 0.052 6024 Dihedral : 5.880 22.928 4424 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.69 % Allowed : 4.65 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 0.24 (0.13), residues: 4028 helix: -0.54 (0.21), residues: 548 sheet: 0.27 (0.14), residues: 1356 loop : 0.46 (0.14), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 236 TYR 0.026 0.003 TYR A 106 PHE 0.020 0.002 PHE A 995 TRP 0.047 0.003 TRP C 559 HIS 0.007 0.002 HIS D 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.23 (33460) covalent geometry : angle 0.73773 / 0.40 (45644) hydrogen bonds : bond 0.06266 / 4.09 ( 1201) hydrogen bonds : angle 6.39108 / 4.43 ( 3300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 479 time to evaluate : 1.527 Fit side-chains REVERT: B 975 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6710 (mt-10) REVERT: D 975 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6724 (mt-10) outliers start: 24 outliers final: 7 residues processed: 496 average time/residue: 0.9556 time to fit residues: 543.8047 Evaluate side-chains 474 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 467 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 245 optimal weight: 4.9990 chunk 367 optimal weight: 0.2980 chunk 216 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 70 optimal weight: 0.0060 chunk 179 optimal weight: 0.9990 chunk 322 optimal weight: 0.9990 chunk 270 optimal weight: 10.0000 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 652 HIS A 710 ASN A 823 GLN A 891 ASN A 955 HIS B 18 GLN B 652 HIS B 710 ASN B 823 GLN B 830 GLN B 891 ASN B 955 HIS C 18 GLN C 652 HIS C 710 ASN C 823 GLN C 830 GLN C 891 ASN C 955 HIS D 652 HIS D 710 ASN D 823 GLN D 830 GLN D 891 ASN D 955 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.189516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.163068 restraints weight = 10786.512| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 0.32 r_work: 0.3509 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.3300 rms_B_bonded: 2.42 restraints_weight: 0.1250 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33460 Z= 0.134 Angle : 0.591 7.797 45644 Z= 0.321 Chirality : 0.045 0.149 4768 Planarity : 0.004 0.031 6024 Dihedral : 5.505 21.268 4424 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.75 % Allowed : 5.02 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 0.37 (0.13), residues: 4028 helix: -0.31 (0.21), residues: 548 sheet: 0.34 (0.14), residues: 1320 loop : 0.52 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 605 TYR 0.021 0.002 TYR C 106 PHE 0.012 0.001 PHE D 995 TRP 0.042 0.002 TRP D 559 HIS 0.003 0.001 HIS C 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (33460) covalent geometry : angle 0.59148 / 0.32 (45644) hydrogen bonds : bond 0.04742 / 3.11 ( 1201) hydrogen bonds : angle 6.00667 / 4.17 ( 3300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 466 time to evaluate : 1.410 Fit side-chains REVERT: D 751 MET cc_start: 0.4538 (mmm) cc_final: 0.4290 (mmm) outliers start: 26 outliers final: 10 residues processed: 485 average time/residue: 0.8777 time to fit residues: 490.1387 Evaluate side-chains 475 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 465 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 281 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 384 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 chunk 271 optimal weight: 0.5980 chunk 338 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 282 optimal weight: 0.0570 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 HIS A 710 ASN A 823 GLN A 891 ASN A 955 HIS B 652 HIS B 710 ASN B 823 GLN B 830 GLN B 891 ASN B 955 HIS C 18 GLN C 652 HIS C 710 ASN C 823 GLN C 830 GLN C 891 ASN C 955 HIS D 652 HIS D 710 ASN D 823 GLN D 830 GLN D 891 ASN D 955 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.187866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.160931 restraints weight = 10698.911| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 0.32 r_work: 0.3481 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.3285 rms_B_bonded: 2.19 restraints_weight: 0.1250 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33460 Z= 0.156 Angle : 0.627 8.260 45644 Z= 0.340 Chirality : 0.046 0.152 4768 Planarity : 0.004 0.033 6024 Dihedral : 5.607 21.824 4424 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.78 % Allowed : 4.97 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 4028 helix: -0.36 (0.21), residues: 548 sheet: 0.32 (0.14), residues: 1344 loop : 0.54 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 298 TYR 0.023 0.002 TYR C 106 PHE 0.014 0.002 PHE A 995 TRP 0.040 0.002 TRP C 559 HIS 0.005 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (33460) covalent geometry : angle 0.62729 / 0.34 (45644) hydrogen bonds : bond 0.05128 / 3.36 ( 1201) hydrogen bonds : angle 6.09583 / 4.23 ( 3300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 474 time to evaluate : 1.432 Fit side-chains REVERT: D 751 MET cc_start: 0.4552 (mmm) cc_final: 0.4280 (mmm) outliers start: 27 outliers final: 8 residues processed: 492 average time/residue: 0.9681 time to fit residues: 547.6582 Evaluate side-chains 475 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 467 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 340 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 313 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 402 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 HIS A 710 ASN A 823 GLN A 891 ASN A 955 HIS B 652 HIS B 710 ASN B 823 GLN B 830 GLN B 891 ASN B 955 HIS C 652 HIS C 710 ASN C 823 GLN C 830 GLN C 891 ASN C 955 HIS D 652 HIS D 710 ASN D 823 GLN D 830 GLN D 891 ASN D 955 HIS ** D1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.184003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.156662 restraints weight = 10554.401| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 0.33 r_work: 0.3417 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 1.10 restraints_weight: 0.2500 r_work: 0.3209 rms_B_bonded: 2.33 restraints_weight: 0.1250 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 33460 Z= 0.279 Angle : 0.814 9.695 45644 Z= 0.442 Chirality : 0.051 0.162 4768 Planarity : 0.007 0.060 6024 Dihedral : 5.995 23.402 4424 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.69 % Allowed : 5.11 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 0.14 (0.13), residues: 4028 helix: -0.66 (0.21), residues: 548 sheet: 0.20 (0.14), residues: 1292 loop : 0.40 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 316 TYR 0.027 0.004 TYR C 106 PHE 0.022 0.003 PHE B 995 TRP 0.053 0.004 TRP B 559 HIS 0.009 0.002 HIS B 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.28 (33460) covalent geometry : angle 0.81434 / 0.44 (45644) hydrogen bonds : bond 0.06862 / 4.47 ( 1201) hydrogen bonds : angle 6.50908 / 4.51 ( 3300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 480 time to evaluate : 1.439 Fit side-chains outliers start: 24 outliers final: 7 residues processed: 495 average time/residue: 0.9561 time to fit residues: 542.7731 Evaluate side-chains 475 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 468 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 46 optimal weight: 3.9990 chunk 354 optimal weight: 0.9980 chunk 336 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 339 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 652 HIS A 710 ASN A 823 GLN A 891 ASN A 955 HIS B 18 GLN B 652 HIS B 710 ASN B 823 GLN B 830 GLN B 891 ASN B 955 HIS C 18 GLN C 652 HIS C 710 ASN C 823 GLN C 830 GLN C 891 ASN C 955 HIS D 18 GLN D 652 HIS D 710 ASN D 823 GLN D 830 GLN D 891 ASN D 955 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.186446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.159244 restraints weight = 10679.151| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 0.33 r_work: 0.3454 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 1.09 restraints_weight: 0.2500 r_work: 0.3255 rms_B_bonded: 2.24 restraints_weight: 0.1250 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33460 Z= 0.181 Angle : 0.676 8.680 45644 Z= 0.367 Chirality : 0.047 0.156 4768 Planarity : 0.005 0.038 6024 Dihedral : 5.790 22.622 4424 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.43 % Allowed : 5.40 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 0.27 (0.13), residues: 4028 helix: -0.54 (0.21), residues: 548 sheet: 0.26 (0.14), residues: 1344 loop : 0.50 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 605 TYR 0.024 0.003 TYR A 106 PHE 0.016 0.002 PHE C 995 TRP 0.044 0.002 TRP C 559 HIS 0.005 0.001 HIS B 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (33460) covalent geometry : angle 0.67583 / 0.37 (45644) hydrogen bonds : bond 0.05636 / 3.69 ( 1201) hydrogen bonds : angle 6.24437 / 4.33 ( 3300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8056 Ramachandran restraints generated. 4028 Oldfield, 0 Emsley, 4028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 474 time to evaluate : 1.487 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 481 average time/residue: 0.9790 time to fit residues: 540.3069 Evaluate side-chains 470 residues out of total 3464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 463 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 374 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 161 optimal weight: 0.1980 chunk 266 optimal weight: 0.9980 chunk 324 optimal weight: 0.6980 chunk 314 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 HIS A 710 ASN A 823 GLN A 891 ASN A 955 HIS B 652 HIS B 710 ASN B 823 GLN B 830 GLN B 891 ASN B 955 HIS C 18 GLN C 652 HIS C 710 ASN C 823 GLN C 830 GLN C 891 ASN C 955 HIS D 18 GLN D 652 HIS D 710 ASN D 823 GLN D 830 GLN D 891 ASN D 955 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.189406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.161400 restraints weight = 10717.756| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 0.34 r_work: 0.3490 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 1.09 restraints_weight: 0.2500 r_work: 0.3295 rms_B_bonded: 2.30 restraints_weight: 0.1250 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33460 Z= 0.134 Angle : 0.600 7.630 45644 Z= 0.324 Chirality : 0.046 0.152 4768 Planarity : 0.004 0.031 6024 Dihedral : 5.533 21.392 4424 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.66 % Allowed : 5.11 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.32 % 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: 4028 helix: -0.35 (0.21), residues: 548 sheet: 0.32 (0.14), residues: 1320 loop : 0.53 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 605 TYR 0.022 0.002 TYR A 106 PHE 0.011 0.001 PHE A 607 TRP 0.044 0.002 TRP C 559 HIS 0.004 0.001 HIS D 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (33460) covalent geometry : angle 0.59993 / 0.32 (45644) hydrogen bonds : bond 0.04721 / 3.10 ( 1201) hydrogen bonds : angle 6.01051 / 4.17 ( 3300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36826.10 seconds wall clock time: 621 minutes 20.59 seconds (37280.59 seconds total)