Starting phenix.real_space_refine on Mon Nov 18 10:48:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ts6_41590/11_2024/8ts6_41590_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ts6_41590/11_2024/8ts6_41590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ts6_41590/11_2024/8ts6_41590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ts6_41590/11_2024/8ts6_41590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ts6_41590/11_2024/8ts6_41590_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ts6_41590/11_2024/8ts6_41590_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 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 180 5.16 5 C 31032 2.51 5 N 7908 2.21 5 O 9324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 48444 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "C" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "D" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "E" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "F" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "G" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "H" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "I" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "J" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "K" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Chain: "L" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4037 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 15, 'TRANS': 484} Chain breaks: 2 Time building chain proxies: 25.38, per 1000 atoms: 0.52 Number of scatterers: 48444 At special positions: 0 Unit cell: (191.53, 191.53, 133.75, 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 180 16.00 O 9324 8.00 N 7908 7.00 C 31032 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: 11.85 Conformation dependent library (CDL) restraints added in 5.7 seconds 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11424 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 72 sheets defined 54.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 16 through 35 Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 36 through 39 Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.689A pdb=" N LEU A 45 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.750A pdb=" N TRP A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 280 through 301 Processing helix chain 'A' and resid 333 through 346 Processing helix chain 'A' and resid 366 through 386 removed outlier: 4.281A pdb=" N ILE A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.557A pdb=" N LYS A 392 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 439 removed outlier: 3.779A pdb=" N ALA A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 473 removed outlier: 3.515A pdb=" N LEU A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.575A pdb=" N LEU A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 527 removed outlier: 3.548A pdb=" N ASP A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 16 through 35 Proline residue: B 24 - end of helix Processing helix chain 'B' and resid 36 through 39 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.702A pdb=" N LEU B 45 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.751A pdb=" N TRP B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 276 through 279 Processing helix chain 'B' and resid 280 through 301 Processing helix chain 'B' and resid 333 through 346 Processing helix chain 'B' and resid 366 through 386 removed outlier: 4.294A pdb=" N ILE B 386 " --> pdb=" O ILE B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.610A pdb=" N LYS B 392 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 439 removed outlier: 3.788A pdb=" N ALA B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.534A pdb=" N LEU B 473 " --> pdb=" O ARG B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 479 through 495 removed outlier: 3.587A pdb=" N LEU B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 527 removed outlier: 3.539A pdb=" N ASP B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 16 through 35 Proline residue: C 24 - end of helix Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.751A pdb=" N LEU C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 61 Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 95 through 105 removed outlier: 3.782A pdb=" N TRP C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 127 Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 276 through 279 Processing helix chain 'C' and resid 280 through 301 Processing helix chain 'C' and resid 333 through 346 Processing helix chain 'C' and resid 366 through 386 removed outlier: 4.273A pdb=" N ILE C 386 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.632A pdb=" N LYS C 392 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 439 removed outlier: 3.785A pdb=" N ALA C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 473 removed outlier: 4.235A pdb=" N GLN C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 473 " --> pdb=" O ARG C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 495 removed outlier: 3.587A pdb=" N LEU C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 527 Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 16 through 35 Proline residue: D 24 - end of helix Processing helix chain 'D' and resid 36 through 39 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.701A pdb=" N LEU D 45 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 89 through 92 Processing helix chain 'D' and resid 95 through 105 removed outlier: 3.745A pdb=" N TRP D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'D' and resid 276 through 279 Processing helix chain 'D' and resid 280 through 302 Processing helix chain 'D' and resid 333 through 346 Processing helix chain 'D' and resid 366 through 386 removed outlier: 4.296A pdb=" N ILE D 386 " --> pdb=" O ILE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 394 removed outlier: 3.584A pdb=" N LYS D 392 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 439 removed outlier: 3.770A pdb=" N ALA D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.514A pdb=" N LEU D 473 " --> pdb=" O ARG D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 479 through 495 removed outlier: 3.565A pdb=" N LEU D 483 " --> pdb=" O PRO D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 527 removed outlier: 3.518A pdb=" N ASP D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 16 through 35 Proline residue: E 24 - end of helix Processing helix chain 'E' and resid 36 through 39 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.701A pdb=" N LEU E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 61 Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 89 through 92 Processing helix chain 'E' and resid 95 through 105 removed outlier: 3.754A pdb=" N TRP E 99 " --> pdb=" O ASP E 95 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS E 105 " --> pdb=" O SER E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 127 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 276 through 279 Processing helix chain 'E' and resid 280 through 301 Processing helix chain 'E' and resid 333 through 346 Processing helix chain 'E' and resid 366 through 386 removed outlier: 4.294A pdb=" N ILE E 386 " --> pdb=" O ILE E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 removed outlier: 3.611A pdb=" N LYS E 392 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 439 removed outlier: 3.785A pdb=" N ALA E 416 " --> pdb=" O VAL E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 473 removed outlier: 3.548A pdb=" N LEU E 473 " --> pdb=" O ARG E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 Processing helix chain 'E' and resid 479 through 495 removed outlier: 3.603A pdb=" N LEU E 483 " --> pdb=" O PRO E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 527 removed outlier: 3.524A pdb=" N ASP E 527 " --> pdb=" O LYS E 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 16 through 35 Proline residue: F 24 - end of helix Processing helix chain 'F' and resid 36 through 39 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.726A pdb=" N LEU F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 61 Processing helix chain 'F' and resid 67 through 82 Processing helix chain 'F' and resid 89 through 92 Processing helix chain 'F' and resid 95 through 105 removed outlier: 3.802A pdb=" N TRP F 99 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS F 105 " --> pdb=" O SER F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 164 through 166 No H-bonds generated for 'chain 'F' and resid 164 through 166' Processing helix chain 'F' and resid 276 through 279 Processing helix chain 'F' and resid 280 through 302 Processing helix chain 'F' and resid 333 through 346 Processing helix chain 'F' and resid 366 through 386 removed outlier: 4.265A pdb=" N ILE F 386 " --> pdb=" O ILE F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 removed outlier: 3.586A pdb=" N LYS F 392 " --> pdb=" O ASN F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 439 removed outlier: 3.791A pdb=" N ALA F 416 " --> pdb=" O VAL F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 473 removed outlier: 4.227A pdb=" N GLN F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 473 " --> pdb=" O ARG F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 478 Processing helix chain 'F' and resid 479 through 495 removed outlier: 3.578A pdb=" N LEU F 483 " --> pdb=" O PRO F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 527 removed outlier: 3.562A pdb=" N ASP F 527 " --> pdb=" O LYS F 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 16 through 35 Proline residue: G 24 - end of helix Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.696A pdb=" N LEU G 45 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 89 through 92 Processing helix chain 'G' and resid 95 through 105 removed outlier: 3.730A pdb=" N TRP G 99 " --> pdb=" O ASP G 95 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS G 105 " --> pdb=" O SER G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 127 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 164 through 166 No H-bonds generated for 'chain 'G' and resid 164 through 166' Processing helix chain 'G' and resid 276 through 279 Processing helix chain 'G' and resid 280 through 302 Processing helix chain 'G' and resid 333 through 346 Processing helix chain 'G' and resid 366 through 386 removed outlier: 4.277A pdb=" N ILE G 386 " --> pdb=" O ILE G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 394 removed outlier: 3.606A pdb=" N LYS G 392 " --> pdb=" O ASN G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 439 removed outlier: 3.778A pdb=" N ALA G 416 " --> pdb=" O VAL G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 473 Processing helix chain 'G' and resid 474 through 478 Processing helix chain 'G' and resid 479 through 495 removed outlier: 3.578A pdb=" N LEU G 483 " --> pdb=" O PRO G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 527 removed outlier: 3.514A pdb=" N ASP G 527 " --> pdb=" O LYS G 523 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 13 Processing helix chain 'H' and resid 16 through 35 Proline residue: H 24 - end of helix Processing helix chain 'H' and resid 36 through 39 Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.700A pdb=" N LEU H 45 " --> pdb=" O GLU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 61 Processing helix chain 'H' and resid 67 through 82 Processing helix chain 'H' and resid 89 through 92 Processing helix chain 'H' and resid 95 through 105 removed outlier: 3.784A pdb=" N TRP H 99 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS H 105 " --> pdb=" O SER H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 127 Processing helix chain 'H' and resid 145 through 155 Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'H' and resid 276 through 279 Processing helix chain 'H' and resid 280 through 302 Processing helix chain 'H' and resid 333 through 346 Processing helix chain 'H' and resid 366 through 386 removed outlier: 4.297A pdb=" N ILE H 386 " --> pdb=" O ILE H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 394 removed outlier: 3.610A pdb=" N LYS H 392 " --> pdb=" O ASN H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 439 removed outlier: 3.785A pdb=" N ALA H 416 " --> pdb=" O VAL H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 473 removed outlier: 3.545A pdb=" N LEU H 473 " --> pdb=" O ARG H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 478 Processing helix chain 'H' and resid 479 through 495 removed outlier: 3.589A pdb=" N LEU H 483 " --> pdb=" O PRO H 479 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 527 Processing helix chain 'I' and resid 9 through 13 Processing helix chain 'I' and resid 16 through 35 Proline residue: I 24 - end of helix Processing helix chain 'I' and resid 36 through 39 Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.750A pdb=" N LEU I 45 " --> pdb=" O GLU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 61 Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 89 through 92 Processing helix chain 'I' and resid 95 through 105 removed outlier: 3.764A pdb=" N TRP I 99 " --> pdb=" O ASP I 95 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 127 Processing helix chain 'I' and resid 145 through 155 Processing helix chain 'I' and resid 164 through 166 No H-bonds generated for 'chain 'I' and resid 164 through 166' Processing helix chain 'I' and resid 276 through 279 Processing helix chain 'I' and resid 280 through 302 Processing helix chain 'I' and resid 333 through 346 Processing helix chain 'I' and resid 366 through 386 removed outlier: 4.263A pdb=" N ILE I 386 " --> pdb=" O ILE I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 394 removed outlier: 3.620A pdb=" N LYS I 392 " --> pdb=" O ASN I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 439 removed outlier: 3.791A pdb=" N ALA I 416 " --> pdb=" O VAL I 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 458 through 473 removed outlier: 4.239A pdb=" N GLN I 462 " --> pdb=" O ARG I 458 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU I 473 " --> pdb=" O ARG I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 478 Processing helix chain 'I' and resid 479 through 495 removed outlier: 3.591A pdb=" N LEU I 483 " --> pdb=" O PRO I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 527 Processing helix chain 'J' and resid 9 through 13 Processing helix chain 'J' and resid 16 through 35 Proline residue: J 24 - end of helix Processing helix chain 'J' and resid 36 through 39 Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.697A pdb=" N LEU J 45 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 61 Processing helix chain 'J' and resid 67 through 82 Processing helix chain 'J' and resid 89 through 92 Processing helix chain 'J' and resid 95 through 105 removed outlier: 3.793A pdb=" N TRP J 99 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS J 105 " --> pdb=" O SER J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 127 Processing helix chain 'J' and resid 145 through 155 Processing helix chain 'J' and resid 164 through 166 No H-bonds generated for 'chain 'J' and resid 164 through 166' Processing helix chain 'J' and resid 276 through 279 Processing helix chain 'J' and resid 280 through 301 Processing helix chain 'J' and resid 333 through 346 Processing helix chain 'J' and resid 366 through 386 removed outlier: 4.290A pdb=" N ILE J 386 " --> pdb=" O ILE J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 394 removed outlier: 3.552A pdb=" N LYS J 392 " --> pdb=" O ASN J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 439 removed outlier: 3.754A pdb=" N ALA J 416 " --> pdb=" O VAL J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 458 through 473 removed outlier: 4.259A pdb=" N GLN J 462 " --> pdb=" O ARG J 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU J 473 " --> pdb=" O ARG J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 478 Processing helix chain 'J' and resid 479 through 495 removed outlier: 3.563A pdb=" N LEU J 483 " --> pdb=" O PRO J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 527 removed outlier: 3.546A pdb=" N ASP J 527 " --> pdb=" O LYS J 523 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 16 through 35 Proline residue: K 24 - end of helix Processing helix chain 'K' and resid 36 through 39 Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.699A pdb=" N LEU K 45 " --> pdb=" O GLU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 61 Processing helix chain 'K' and resid 67 through 82 Processing helix chain 'K' and resid 89 through 92 Processing helix chain 'K' and resid 95 through 105 removed outlier: 3.745A pdb=" N TRP K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS K 105 " --> pdb=" O SER K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 164 through 166 No H-bonds generated for 'chain 'K' and resid 164 through 166' Processing helix chain 'K' and resid 276 through 279 Processing helix chain 'K' and resid 280 through 302 Processing helix chain 'K' and resid 333 through 346 Processing helix chain 'K' and resid 366 through 386 removed outlier: 4.294A pdb=" N ILE K 386 " --> pdb=" O ILE K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 389 through 394 removed outlier: 3.614A pdb=" N LYS K 392 " --> pdb=" O ASN K 389 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 439 removed outlier: 3.782A pdb=" N ALA K 416 " --> pdb=" O VAL K 412 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 473 removed outlier: 3.554A pdb=" N LEU K 473 " --> pdb=" O ARG K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 478 Processing helix chain 'K' and resid 479 through 495 removed outlier: 3.589A pdb=" N LEU K 483 " --> pdb=" O PRO K 479 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 527 removed outlier: 3.539A pdb=" N ASP K 527 " --> pdb=" O LYS K 523 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 13 Processing helix chain 'L' and resid 16 through 35 Proline residue: L 24 - end of helix Processing helix chain 'L' and resid 36 through 39 Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.754A pdb=" N LEU L 45 " --> pdb=" O GLU L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 61 Processing helix chain 'L' and resid 67 through 82 Processing helix chain 'L' and resid 89 through 92 Processing helix chain 'L' and resid 95 through 105 removed outlier: 3.784A pdb=" N TRP L 99 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS L 105 " --> pdb=" O SER L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 127 Processing helix chain 'L' and resid 145 through 155 Processing helix chain 'L' and resid 164 through 166 No H-bonds generated for 'chain 'L' and resid 164 through 166' Processing helix chain 'L' and resid 276 through 279 Processing helix chain 'L' and resid 280 through 301 Processing helix chain 'L' and resid 333 through 346 Processing helix chain 'L' and resid 366 through 386 removed outlier: 3.617A pdb=" N MET L 370 " --> pdb=" O THR L 366 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE L 386 " --> pdb=" O ILE L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 394 removed outlier: 3.631A pdb=" N LYS L 392 " --> pdb=" O ASN L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 439 removed outlier: 3.786A pdb=" N ALA L 416 " --> pdb=" O VAL L 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 458 through 473 removed outlier: 4.231A pdb=" N GLN L 462 " --> pdb=" O ARG L 458 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 473 " --> pdb=" O ARG L 469 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 478 Processing helix chain 'L' and resid 479 through 495 removed outlier: 3.590A pdb=" N LEU L 483 " --> pdb=" O PRO L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 527 removed outlier: 3.508A pdb=" N ASP L 527 " --> pdb=" O LYS L 523 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 163 removed outlier: 4.206A pdb=" N TYR A 131 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 174 removed outlier: 5.644A pdb=" N ILE A 168 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS A 184 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP A 174 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 218 through 220 removed outlier: 3.745A pdb=" N LYS A 228 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 362 removed outlier: 8.270A pdb=" N ILE L 353 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS A 306 " --> pdb=" O ILE L 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 353 Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 163 removed outlier: 4.180A pdb=" N TYR B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 168 through 174 removed outlier: 5.682A pdb=" N ILE B 168 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS B 184 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 174 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.537A pdb=" N ILE B 219 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 352 through 353 Processing sheet with id=AB5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB6, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AB7, first strand: chain 'C' and resid 159 through 163 removed outlier: 4.222A pdb=" N TYR C 131 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 168 through 174 removed outlier: 5.649A pdb=" N ILE C 168 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS C 184 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP C 174 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 218 through 220 removed outlier: 6.529A pdb=" N ILE C 219 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 352 through 353 Processing sheet with id=AC2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AC3, first strand: chain 'D' and resid 7 through 8 Processing sheet with id=AC4, first strand: chain 'D' and resid 159 through 163 removed outlier: 4.206A pdb=" N TYR D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 168 through 174 removed outlier: 5.666A pdb=" N ILE D 168 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS D 184 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP D 174 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 218 through 220 removed outlier: 6.541A pdb=" N ILE D 219 " --> pdb=" O SER D 227 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 352 through 353 Processing sheet with id=AC8, first strand: chain 'D' and resid 449 through 451 Processing sheet with id=AC9, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AD1, first strand: chain 'E' and resid 159 through 163 removed outlier: 4.178A pdb=" N TYR E 131 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 168 through 174 removed outlier: 5.687A pdb=" N ILE E 168 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS E 184 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP E 174 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 218 through 220 removed outlier: 6.543A pdb=" N ILE E 219 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 352 through 353 Processing sheet with id=AD5, first strand: chain 'E' and resid 449 through 451 Processing sheet with id=AD6, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AD7, first strand: chain 'F' and resid 159 through 163 removed outlier: 4.224A pdb=" N TYR F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 168 through 174 removed outlier: 5.657A pdb=" N ILE F 168 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS F 184 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP F 174 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 218 through 220 removed outlier: 6.530A pdb=" N ILE F 219 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 352 through 353 Processing sheet with id=AE2, first strand: chain 'F' and resid 449 through 451 Processing sheet with id=AE3, first strand: chain 'G' and resid 7 through 8 Processing sheet with id=AE4, first strand: chain 'G' and resid 159 through 163 removed outlier: 4.206A pdb=" N TYR G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 168 through 174 removed outlier: 5.653A pdb=" N ILE G 168 " --> pdb=" O LYS G 184 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS G 184 " --> pdb=" O ILE G 168 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP G 174 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 218 through 220 removed outlier: 6.538A pdb=" N ILE G 219 " --> pdb=" O SER G 227 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 352 through 353 Processing sheet with id=AE8, first strand: chain 'G' and resid 449 through 451 Processing sheet with id=AE9, first strand: chain 'H' and resid 7 through 8 Processing sheet with id=AF1, first strand: chain 'H' and resid 159 through 163 removed outlier: 4.173A pdb=" N TYR H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 168 through 174 removed outlier: 5.662A pdb=" N ILE H 168 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS H 184 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP H 174 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 218 through 220 removed outlier: 6.540A pdb=" N ILE H 219 " --> pdb=" O SER H 227 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 352 through 353 Processing sheet with id=AF5, first strand: chain 'H' and resid 449 through 451 Processing sheet with id=AF6, first strand: chain 'I' and resid 7 through 8 Processing sheet with id=AF7, first strand: chain 'I' and resid 159 through 163 removed outlier: 4.225A pdb=" N TYR I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 168 through 174 removed outlier: 5.647A pdb=" N ILE I 168 " --> pdb=" O LYS I 184 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS I 184 " --> pdb=" O ILE I 168 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP I 174 " --> pdb=" O ILE I 178 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE I 178 " --> pdb=" O ASP I 174 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 218 through 220 removed outlier: 6.528A pdb=" N ILE I 219 " --> pdb=" O SER I 227 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 352 through 353 Processing sheet with id=AG2, first strand: chain 'I' and resid 449 through 451 Processing sheet with id=AG3, first strand: chain 'J' and resid 7 through 8 Processing sheet with id=AG4, first strand: chain 'J' and resid 159 through 163 removed outlier: 4.198A pdb=" N TYR J 131 " --> pdb=" O ILE J 163 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 168 through 174 removed outlier: 5.663A pdb=" N ILE J 168 " --> pdb=" O LYS J 184 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS J 184 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP J 174 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 218 through 220 removed outlier: 6.535A pdb=" N ILE J 219 " --> pdb=" O SER J 227 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 352 through 353 Processing sheet with id=AG8, first strand: chain 'J' and resid 449 through 451 Processing sheet with id=AG9, first strand: chain 'K' and resid 7 through 8 Processing sheet with id=AH1, first strand: chain 'K' and resid 159 through 163 removed outlier: 4.180A pdb=" N TYR K 131 " --> pdb=" O ILE K 163 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 168 through 174 removed outlier: 5.674A pdb=" N ILE K 168 " --> pdb=" O LYS K 184 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS K 184 " --> pdb=" O ILE K 168 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP K 174 " --> pdb=" O ILE K 178 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE K 178 " --> pdb=" O ASP K 174 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 218 through 220 removed outlier: 6.537A pdb=" N ILE K 219 " --> pdb=" O SER K 227 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 352 through 353 Processing sheet with id=AH5, first strand: chain 'K' and resid 449 through 451 Processing sheet with id=AH6, first strand: chain 'L' and resid 7 through 8 Processing sheet with id=AH7, first strand: chain 'L' and resid 159 through 163 removed outlier: 4.221A pdb=" N TYR L 131 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 168 through 174 removed outlier: 5.648A pdb=" N ILE L 168 " --> pdb=" O LYS L 184 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS L 184 " --> pdb=" O ILE L 168 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP L 174 " --> pdb=" O ILE L 178 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE L 178 " --> pdb=" O ASP L 174 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 218 through 220 removed outlier: 6.529A pdb=" N ILE L 219 " --> pdb=" O SER L 227 " (cutoff:3.500A) 2756 hydrogen bonds defined for protein. 7695 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: 23.87 Time building geometry restraints manager: 13.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15611 1.34 - 1.46: 8593 1.46 - 1.57: 24864 1.57 - 1.69: 0 1.69 - 1.81: 324 Bond restraints: 49392 Sorted by residual: bond pdb=" C ILE K 308 " pdb=" N ARG K 309 " ideal model delta sigma weight residual 1.332 1.315 0.017 7.50e-03 1.78e+04 5.19e+00 bond pdb=" C ILE H 308 " pdb=" N ARG H 309 " ideal model delta sigma weight residual 1.331 1.314 0.016 9.80e-03 1.04e+04 2.75e+00 bond pdb=" C ILE B 308 " pdb=" N ARG B 309 " ideal model delta sigma weight residual 1.331 1.314 0.016 9.80e-03 1.04e+04 2.74e+00 bond pdb=" C ILE J 308 " pdb=" N ARG J 309 " ideal model delta sigma weight residual 1.331 1.315 0.016 9.80e-03 1.04e+04 2.68e+00 bond pdb=" C ILE D 308 " pdb=" N ARG D 309 " ideal model delta sigma weight residual 1.331 1.315 0.016 9.80e-03 1.04e+04 2.61e+00 ... (remaining 49387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 64081 1.03 - 2.06: 2220 2.06 - 3.08: 377 3.08 - 4.11: 17 4.11 - 5.14: 13 Bond angle restraints: 66708 Sorted by residual: angle pdb=" N THR A 366 " pdb=" CA THR A 366 " pdb=" C THR A 366 " ideal model delta sigma weight residual 114.56 109.42 5.14 1.27e+00 6.20e-01 1.64e+01 angle pdb=" N LYS J 341 " pdb=" CA LYS J 341 " pdb=" C LYS J 341 " ideal model delta sigma weight residual 111.07 107.86 3.21 1.07e+00 8.73e-01 8.98e+00 angle pdb=" N LYS D 341 " pdb=" CA LYS D 341 " pdb=" C LYS D 341 " ideal model delta sigma weight residual 111.07 108.04 3.03 1.07e+00 8.73e-01 7.99e+00 angle pdb=" N LYS G 341 " pdb=" CA LYS G 341 " pdb=" C LYS G 341 " ideal model delta sigma weight residual 111.07 108.08 2.99 1.07e+00 8.73e-01 7.82e+00 angle pdb=" N LYS B 341 " pdb=" CA LYS B 341 " pdb=" C LYS B 341 " ideal model delta sigma weight residual 111.07 108.15 2.92 1.07e+00 8.73e-01 7.44e+00 ... (remaining 66703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 27146 15.29 - 30.58: 1996 30.58 - 45.87: 517 45.87 - 61.17: 211 61.17 - 76.46: 34 Dihedral angle restraints: 29904 sinusoidal: 12180 harmonic: 17724 Sorted by residual: dihedral pdb=" CA ALA I 385 " pdb=" C ALA I 385 " pdb=" N ILE I 386 " pdb=" CA ILE I 386 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA F 385 " pdb=" C ALA F 385 " pdb=" N ILE F 386 " pdb=" CA ILE F 386 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ALA C 385 " pdb=" C ALA C 385 " pdb=" N ILE C 386 " pdb=" CA ILE C 386 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 29901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 4227 0.026 - 0.052: 1917 0.052 - 0.079: 794 0.079 - 0.105: 300 0.105 - 0.131: 178 Chirality restraints: 7416 Sorted by residual: chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE F 189 " pdb=" N ILE F 189 " pdb=" C ILE F 189 " pdb=" CB ILE F 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 7413 not shown) Planarity restraints: 8496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN I 337 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C ASN I 337 " 0.024 2.00e-02 2.50e+03 pdb=" O ASN I 337 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU I 338 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 337 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C ASN L 337 " -0.022 2.00e-02 2.50e+03 pdb=" O ASN L 337 " 0.008 2.00e-02 2.50e+03 pdb=" N GLU L 338 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 337 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C ASN H 337 " 0.022 2.00e-02 2.50e+03 pdb=" O ASN H 337 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU H 338 " -0.008 2.00e-02 2.50e+03 ... (remaining 8493 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 7954 2.76 - 3.29: 51197 3.29 - 3.83: 84684 3.83 - 4.36: 98485 4.36 - 4.90: 165968 Nonbonded interactions: 408288 Sorted by model distance: nonbonded pdb=" OE1 GLU B 350 " pdb=" NH2 ARG E 48 " model vdw 2.221 3.120 nonbonded pdb=" O LEU B 79 " pdb=" OG SER B 82 " model vdw 2.221 3.040 nonbonded pdb=" O LEU H 79 " pdb=" OG SER H 82 " model vdw 2.223 3.040 nonbonded pdb=" O LEU G 79 " pdb=" OG SER G 82 " model vdw 2.223 3.040 nonbonded pdb=" O LEU C 79 " pdb=" OG SER C 82 " model vdw 2.224 3.040 ... (remaining 408283 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.060 Extract box with map and model: 1.820 Check model and map are aligned: 0.360 Set scattering table: 0.430 Process input model: 104.920 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.380 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 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 : 0.003 0.031 49392 Z= 0.204 Angle : 0.450 5.139 66708 Z= 0.263 Chirality : 0.040 0.131 7416 Planarity : 0.003 0.026 8496 Dihedral : 12.681 76.458 18480 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.90 % Favored : 96.90 % Rotamer: Outliers : 4.65 % Allowed : 4.86 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.12), residues: 5928 helix: 2.35 (0.10), residues: 2940 sheet: -1.34 (0.15), residues: 1008 loop : 0.35 (0.16), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 307 HIS 0.002 0.001 HIS H 433 PHE 0.011 0.001 PHE L 358 TYR 0.011 0.001 TYR I 381 ARG 0.002 0.000 ARG H 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1877 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 1628 time to evaluate : 5.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LEU cc_start: 0.9137 (tp) cc_final: 0.8937 (tp) REVERT: A 18 ASP cc_start: 0.8723 (p0) cc_final: 0.8477 (p0) REVERT: A 20 GLN cc_start: 0.9107 (mt0) cc_final: 0.8839 (mt0) REVERT: A 40 ASP cc_start: 0.8910 (t0) cc_final: 0.8628 (t0) REVERT: A 48 ARG cc_start: 0.6592 (tpt170) cc_final: 0.6006 (tpm170) REVERT: A 110 ASN cc_start: 0.8894 (m-40) cc_final: 0.8523 (m-40) REVERT: A 176 ASP cc_start: 0.8133 (t0) cc_final: 0.7930 (t70) REVERT: A 206 ASP cc_start: 0.8252 (t0) cc_final: 0.7997 (t0) REVERT: A 217 ASP cc_start: 0.8520 (t0) cc_final: 0.8112 (t0) REVERT: A 228 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8768 (mmmm) REVERT: A 458 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8338 (ttp80) REVERT: A 468 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8560 (mt-10) REVERT: A 485 GLU cc_start: 0.8579 (tp30) cc_final: 0.8260 (tp30) REVERT: A 516 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8394 (mt-10) REVERT: A 518 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9397 (mm) REVERT: B 40 ASP cc_start: 0.8836 (t0) cc_final: 0.8531 (t0) REVERT: B 51 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: B 110 ASN cc_start: 0.8861 (m-40) cc_final: 0.8619 (m-40) REVERT: B 206 ASP cc_start: 0.8296 (t0) cc_final: 0.8077 (t0) REVERT: B 217 ASP cc_start: 0.8496 (t0) cc_final: 0.8084 (t0) REVERT: B 228 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8596 (mmmm) REVERT: B 426 GLU cc_start: 0.8038 (tt0) cc_final: 0.7795 (tt0) REVERT: B 468 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 504 ASN cc_start: 0.8358 (m-40) cc_final: 0.8126 (m110) REVERT: C 20 GLN cc_start: 0.9175 (mt0) cc_final: 0.8874 (mt0) REVERT: C 40 ASP cc_start: 0.8886 (t0) cc_final: 0.8591 (t0) REVERT: C 51 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: C 206 ASP cc_start: 0.8315 (t0) cc_final: 0.8084 (t0) REVERT: C 217 ASP cc_start: 0.8500 (t0) cc_final: 0.8165 (t0) REVERT: C 228 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8673 (mmmm) REVERT: C 270 MET cc_start: 0.8400 (ttm) cc_final: 0.7963 (ttm) REVERT: C 379 ARG cc_start: 0.9164 (tmm-80) cc_final: 0.8415 (tmm-80) REVERT: C 462 GLN cc_start: 0.8292 (mt0) cc_final: 0.7930 (mt0) REVERT: C 464 LEU cc_start: 0.9568 (mt) cc_final: 0.9289 (mt) REVERT: C 485 GLU cc_start: 0.8520 (tp30) cc_final: 0.8163 (tp30) REVERT: C 516 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8364 (mt-10) REVERT: D 18 ASP cc_start: 0.8701 (p0) cc_final: 0.8486 (p0) REVERT: D 20 GLN cc_start: 0.9074 (mt0) cc_final: 0.8727 (mt0) REVERT: D 40 ASP cc_start: 0.8930 (t0) cc_final: 0.8639 (t0) REVERT: D 66 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8680 (mt-10) REVERT: D 87 ILE cc_start: 0.9501 (mm) cc_final: 0.8789 (mm) REVERT: D 110 ASN cc_start: 0.8903 (m-40) cc_final: 0.8476 (m-40) REVERT: D 217 ASP cc_start: 0.8537 (t0) cc_final: 0.8112 (t0) REVERT: D 228 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8704 (mmmm) REVERT: D 270 MET cc_start: 0.8450 (ttm) cc_final: 0.8149 (ttm) REVERT: D 426 GLU cc_start: 0.8178 (tt0) cc_final: 0.7935 (tt0) REVERT: D 468 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8522 (mt-10) REVERT: D 485 GLU cc_start: 0.8584 (tp30) cc_final: 0.8303 (tp30) REVERT: D 516 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8394 (mt-10) REVERT: E 40 ASP cc_start: 0.8844 (t0) cc_final: 0.8533 (t0) REVERT: E 51 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: E 206 ASP cc_start: 0.8274 (t0) cc_final: 0.8069 (t0) REVERT: E 217 ASP cc_start: 0.8556 (t0) cc_final: 0.8130 (t0) REVERT: E 228 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8628 (mmmm) REVERT: E 346 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8625 (p) REVERT: E 377 ARG cc_start: 0.9210 (ptm-80) cc_final: 0.8817 (ptm-80) REVERT: E 426 GLU cc_start: 0.8075 (tt0) cc_final: 0.7841 (tt0) REVERT: E 468 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8438 (mt-10) REVERT: F 2 LEU cc_start: 0.9128 (tp) cc_final: 0.8896 (tp) REVERT: F 20 GLN cc_start: 0.9159 (mt0) cc_final: 0.8854 (mt0) REVERT: F 40 ASP cc_start: 0.8881 (t0) cc_final: 0.8603 (t0) REVERT: F 51 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: F 206 ASP cc_start: 0.8294 (t0) cc_final: 0.8065 (t0) REVERT: F 217 ASP cc_start: 0.8577 (t0) cc_final: 0.8301 (t0) REVERT: F 228 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8691 (mmmm) REVERT: F 270 MET cc_start: 0.8404 (ttm) cc_final: 0.7986 (ttm) REVERT: F 379 ARG cc_start: 0.9153 (tmm-80) cc_final: 0.8438 (tmm-80) REVERT: F 485 GLU cc_start: 0.8477 (tp30) cc_final: 0.8110 (tp30) REVERT: F 492 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7411 (ptp-110) REVERT: F 504 ASN cc_start: 0.8280 (m-40) cc_final: 0.7955 (m-40) REVERT: F 516 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8390 (mt-10) REVERT: G 18 ASP cc_start: 0.8733 (p0) cc_final: 0.8483 (p0) REVERT: G 20 GLN cc_start: 0.9094 (mt0) cc_final: 0.8836 (mt0) REVERT: G 40 ASP cc_start: 0.8942 (t0) cc_final: 0.8645 (t0) REVERT: G 206 ASP cc_start: 0.8157 (t0) cc_final: 0.7553 (t0) REVERT: G 207 ASP cc_start: 0.8176 (m-30) cc_final: 0.7609 (m-30) REVERT: G 217 ASP cc_start: 0.8573 (t0) cc_final: 0.8135 (t0) REVERT: G 305 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8574 (tp-100) REVERT: G 458 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8317 (ttp80) REVERT: G 468 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8494 (mt-10) REVERT: G 485 GLU cc_start: 0.8610 (tp30) cc_final: 0.8306 (tp30) REVERT: G 504 ASN cc_start: 0.8191 (m-40) cc_final: 0.7706 (m-40) REVERT: H 40 ASP cc_start: 0.8839 (t0) cc_final: 0.8539 (t0) REVERT: H 51 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: H 110 ASN cc_start: 0.8820 (m-40) cc_final: 0.8558 (m-40) REVERT: H 206 ASP cc_start: 0.8326 (t0) cc_final: 0.8103 (t0) REVERT: H 217 ASP cc_start: 0.8509 (t0) cc_final: 0.8092 (t0) REVERT: H 228 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8601 (mmmm) REVERT: H 346 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8600 (p) REVERT: H 426 GLU cc_start: 0.8069 (tt0) cc_final: 0.7831 (tt0) REVERT: H 468 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8429 (mt-10) REVERT: H 489 GLN cc_start: 0.8358 (tp-100) cc_final: 0.8140 (tp-100) REVERT: H 516 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8292 (mt-10) REVERT: I 2 LEU cc_start: 0.9121 (tp) cc_final: 0.8901 (tp) REVERT: I 20 GLN cc_start: 0.9159 (mt0) cc_final: 0.8867 (mt0) REVERT: I 40 ASP cc_start: 0.8884 (t0) cc_final: 0.8585 (t0) REVERT: I 51 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: I 206 ASP cc_start: 0.8306 (t0) cc_final: 0.8077 (t0) REVERT: I 217 ASP cc_start: 0.8552 (t0) cc_final: 0.8217 (t0) REVERT: I 228 LYS cc_start: 0.8942 (mmmm) cc_final: 0.8675 (mmmm) REVERT: I 270 MET cc_start: 0.8416 (ttm) cc_final: 0.7979 (ttm) REVERT: I 286 MET cc_start: 0.9206 (mmm) cc_final: 0.8743 (mmm) REVERT: I 462 GLN cc_start: 0.8296 (mt0) cc_final: 0.7948 (mt0) REVERT: I 464 LEU cc_start: 0.9562 (mt) cc_final: 0.9291 (mt) REVERT: I 468 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8318 (mt-10) REVERT: I 485 GLU cc_start: 0.8407 (tp30) cc_final: 0.8114 (tp30) REVERT: I 516 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8360 (mt-10) REVERT: J 12 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9458 (mt) REVERT: J 18 ASP cc_start: 0.8766 (p0) cc_final: 0.8524 (p0) REVERT: J 20 GLN cc_start: 0.9075 (mt0) cc_final: 0.8792 (mt0) REVERT: J 40 ASP cc_start: 0.8912 (t0) cc_final: 0.8616 (t0) REVERT: J 48 ARG cc_start: 0.6794 (tpt170) cc_final: 0.5614 (tpt170) REVERT: J 206 ASP cc_start: 0.8203 (t0) cc_final: 0.7937 (t0) REVERT: J 217 ASP cc_start: 0.8594 (t0) cc_final: 0.8162 (t0) REVERT: J 228 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8699 (mmmm) REVERT: J 247 GLU cc_start: 0.8826 (mp0) cc_final: 0.8620 (mp0) REVERT: J 270 MET cc_start: 0.8453 (ttm) cc_final: 0.8153 (ttm) REVERT: J 346 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8455 (p) REVERT: J 350 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6027 (mm-30) REVERT: J 458 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8181 (ttp80) REVERT: J 461 GLU cc_start: 0.8096 (pm20) cc_final: 0.7852 (pm20) REVERT: J 485 GLU cc_start: 0.8539 (tp30) cc_final: 0.8226 (tp30) REVERT: J 523 LYS cc_start: 0.9067 (ptpp) cc_final: 0.8809 (ptpp) REVERT: K 40 ASP cc_start: 0.8836 (t0) cc_final: 0.8533 (t0) REVERT: K 51 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: K 110 ASN cc_start: 0.8850 (m-40) cc_final: 0.8602 (m-40) REVERT: K 206 ASP cc_start: 0.8289 (t0) cc_final: 0.8080 (t0) REVERT: K 217 ASP cc_start: 0.8504 (t0) cc_final: 0.8090 (t0) REVERT: K 228 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8578 (mmmm) REVERT: K 270 MET cc_start: 0.8451 (ttm) cc_final: 0.8245 (ttm) REVERT: K 346 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8634 (p) REVERT: K 426 GLU cc_start: 0.8029 (tt0) cc_final: 0.7791 (tt0) REVERT: K 468 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8423 (mt-10) REVERT: L 20 GLN cc_start: 0.9175 (mt0) cc_final: 0.8871 (mt0) REVERT: L 40 ASP cc_start: 0.8887 (t0) cc_final: 0.8593 (t0) REVERT: L 51 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: L 206 ASP cc_start: 0.8318 (t0) cc_final: 0.8085 (t0) REVERT: L 217 ASP cc_start: 0.8501 (t0) cc_final: 0.8169 (t0) REVERT: L 228 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8671 (mmmm) REVERT: L 270 MET cc_start: 0.8402 (ttm) cc_final: 0.7972 (ttm) REVERT: L 426 GLU cc_start: 0.8170 (tt0) cc_final: 0.7962 (tt0) REVERT: L 462 GLN cc_start: 0.8291 (mt0) cc_final: 0.7931 (mt0) REVERT: L 464 LEU cc_start: 0.9565 (mt) cc_final: 0.9296 (mt) REVERT: L 468 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8306 (mt-10) REVERT: L 485 GLU cc_start: 0.8469 (tp30) cc_final: 0.8072 (tp30) outliers start: 249 outliers final: 100 residues processed: 1748 average time/residue: 0.6330 time to fit residues: 1785.6968 Evaluate side-chains 1476 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1359 time to evaluate : 5.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 492 ARG Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 66 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 305 GLN Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 347 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 346 SER Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 346 SER Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 492 ARG Chi-restraints excluded: chain K residue 508 ASP Chi-restraints excluded: chain K residue 518 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 346 SER Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 0.6980 chunk 454 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 470 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 350 optimal weight: 9.9990 chunk 544 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN A 526 ASN B 300 ASN B 507 ASN C 504 ASN C 507 ASN D 489 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 ASN E 507 ASN F 462 GLN F 489 GLN F 507 ASN G 489 GLN H 296 HIS H 300 ASN H 489 GLN H 504 ASN I 305 GLN I 414 ASN I 504 ASN J 110 ASN ** J 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 526 ASN K 300 ASN K 305 GLN K 504 ASN K 507 ASN L 504 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 49392 Z= 0.200 Angle : 0.503 6.499 66708 Z= 0.276 Chirality : 0.041 0.161 7416 Planarity : 0.003 0.042 8496 Dihedral : 8.077 64.618 6780 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.80 % Favored : 96.00 % Rotamer: Outliers : 3.66 % Allowed : 12.37 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.11), residues: 5928 helix: 2.21 (0.09), residues: 3000 sheet: -1.08 (0.16), residues: 984 loop : -0.09 (0.16), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 307 HIS 0.002 0.001 HIS A 420 PHE 0.014 0.001 PHE L 358 TYR 0.012 0.001 TYR J 381 ARG 0.006 0.000 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 1460 time to evaluate : 6.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9046 (mt0) cc_final: 0.8740 (mt0) REVERT: A 40 ASP cc_start: 0.8932 (t0) cc_final: 0.8576 (t0) REVERT: A 217 ASP cc_start: 0.8746 (t0) cc_final: 0.8437 (t0) REVERT: A 228 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8688 (mmmm) REVERT: A 379 ARG cc_start: 0.9175 (tmm-80) cc_final: 0.8868 (tmm160) REVERT: A 468 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8553 (mt-10) REVERT: A 485 GLU cc_start: 0.8568 (tp30) cc_final: 0.8305 (tp30) REVERT: B 40 ASP cc_start: 0.8854 (t0) cc_final: 0.8437 (t0) REVERT: B 110 ASN cc_start: 0.8940 (m-40) cc_final: 0.8641 (m-40) REVERT: B 161 PHE cc_start: 0.8919 (t80) cc_final: 0.8679 (t80) REVERT: B 217 ASP cc_start: 0.8700 (t0) cc_final: 0.8362 (t0) REVERT: B 228 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8591 (mmmm) REVERT: B 248 LYS cc_start: 0.9001 (mttt) cc_final: 0.8765 (mttt) REVERT: B 376 GLU cc_start: 0.8436 (tp30) cc_final: 0.7512 (tp30) REVERT: B 379 ARG cc_start: 0.9173 (tmm-80) cc_final: 0.8345 (tmm-80) REVERT: B 426 GLU cc_start: 0.8084 (tt0) cc_final: 0.7858 (tt0) REVERT: B 452 MET cc_start: 0.9053 (mmp) cc_final: 0.8421 (mmp) REVERT: B 468 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8554 (mt-10) REVERT: C 20 GLN cc_start: 0.9154 (mt0) cc_final: 0.8843 (mt0) REVERT: C 40 ASP cc_start: 0.8918 (t0) cc_final: 0.8553 (t0) REVERT: C 51 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: C 206 ASP cc_start: 0.8385 (t0) cc_final: 0.8054 (t0) REVERT: C 207 ASP cc_start: 0.8309 (m-30) cc_final: 0.7514 (m-30) REVERT: C 217 ASP cc_start: 0.8647 (t0) cc_final: 0.8311 (t0) REVERT: C 228 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8616 (mmmm) REVERT: C 245 ASP cc_start: 0.8250 (t70) cc_final: 0.6740 (t0) REVERT: C 376 GLU cc_start: 0.8487 (tp30) cc_final: 0.7505 (tp30) REVERT: C 379 ARG cc_start: 0.9168 (tmm-80) cc_final: 0.8308 (tmm-80) REVERT: C 485 GLU cc_start: 0.8536 (tp30) cc_final: 0.8225 (tp30) REVERT: D 20 GLN cc_start: 0.9054 (mt0) cc_final: 0.8726 (mt0) REVERT: D 40 ASP cc_start: 0.8949 (t0) cc_final: 0.8576 (t0) REVERT: D 206 ASP cc_start: 0.8337 (t0) cc_final: 0.8060 (t0) REVERT: D 217 ASP cc_start: 0.8719 (t0) cc_final: 0.8502 (t0) REVERT: D 228 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8649 (mmmm) REVERT: D 270 MET cc_start: 0.8472 (ttm) cc_final: 0.8252 (ttm) REVERT: D 354 MET cc_start: 0.5167 (ptp) cc_final: 0.4835 (ptt) REVERT: D 379 ARG cc_start: 0.9158 (tmm-80) cc_final: 0.8933 (tmm160) REVERT: D 458 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8209 (ttp80) REVERT: D 468 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8557 (mt-10) REVERT: D 485 GLU cc_start: 0.8616 (tp30) cc_final: 0.8326 (tp30) REVERT: D 504 ASN cc_start: 0.8348 (m-40) cc_final: 0.7943 (m-40) REVERT: D 516 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8384 (mt-10) REVERT: E 38 GLU cc_start: 0.8791 (mp0) cc_final: 0.8459 (mp0) REVERT: E 40 ASP cc_start: 0.8864 (t0) cc_final: 0.8436 (t0) REVERT: E 51 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: E 161 PHE cc_start: 0.8934 (t80) cc_final: 0.8727 (t80) REVERT: E 217 ASP cc_start: 0.8715 (t0) cc_final: 0.8377 (t0) REVERT: E 228 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8597 (mmmm) REVERT: E 376 GLU cc_start: 0.8444 (tp30) cc_final: 0.8062 (tp30) REVERT: E 379 ARG cc_start: 0.9174 (tmm-80) cc_final: 0.8910 (ttp-170) REVERT: E 426 GLU cc_start: 0.8099 (tt0) cc_final: 0.7883 (tt0) REVERT: E 468 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8507 (mt-10) REVERT: E 516 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8320 (mt-10) REVERT: F 20 GLN cc_start: 0.9144 (mt0) cc_final: 0.8823 (mt0) REVERT: F 40 ASP cc_start: 0.8917 (t0) cc_final: 0.8548 (t0) REVERT: F 51 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: F 66 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8662 (mt-10) REVERT: F 217 ASP cc_start: 0.8674 (t0) cc_final: 0.8347 (t0) REVERT: F 228 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8621 (mmmm) REVERT: F 346 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8461 (p) REVERT: F 376 GLU cc_start: 0.8447 (tp30) cc_final: 0.7463 (tp30) REVERT: F 377 ARG cc_start: 0.9256 (ptm-80) cc_final: 0.8991 (ptm-80) REVERT: F 379 ARG cc_start: 0.9164 (tmm-80) cc_final: 0.8306 (tmm-80) REVERT: F 485 GLU cc_start: 0.8487 (tp30) cc_final: 0.8219 (tp30) REVERT: F 516 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8336 (mt-10) REVERT: F 522 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8827 (tmtt) REVERT: G 18 ASP cc_start: 0.8790 (p0) cc_final: 0.8537 (p0) REVERT: G 20 GLN cc_start: 0.9011 (mt0) cc_final: 0.8683 (mt0) REVERT: G 40 ASP cc_start: 0.8965 (t0) cc_final: 0.8602 (t0) REVERT: G 206 ASP cc_start: 0.8277 (t0) cc_final: 0.7850 (t0) REVERT: G 207 ASP cc_start: 0.8241 (m-30) cc_final: 0.7608 (m-30) REVERT: G 217 ASP cc_start: 0.8718 (t0) cc_final: 0.8382 (t0) REVERT: G 248 LYS cc_start: 0.8897 (mttt) cc_final: 0.8645 (mttt) REVERT: G 346 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8681 (p) REVERT: G 376 GLU cc_start: 0.8430 (tp30) cc_final: 0.7718 (tp30) REVERT: G 377 ARG cc_start: 0.9290 (ptm-80) cc_final: 0.8962 (ptm-80) REVERT: G 379 ARG cc_start: 0.9194 (tmm-80) cc_final: 0.8843 (tmm-80) REVERT: G 426 GLU cc_start: 0.8143 (tt0) cc_final: 0.7893 (tt0) REVERT: G 468 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8557 (mt-10) REVERT: G 485 GLU cc_start: 0.8628 (tp30) cc_final: 0.8336 (tp30) REVERT: G 504 ASN cc_start: 0.8282 (m-40) cc_final: 0.8022 (m-40) REVERT: H 40 ASP cc_start: 0.8847 (t0) cc_final: 0.8426 (t0) REVERT: H 217 ASP cc_start: 0.8663 (t0) cc_final: 0.8342 (t0) REVERT: H 228 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8604 (mmmm) REVERT: H 245 ASP cc_start: 0.8358 (t70) cc_final: 0.7145 (t70) REVERT: H 376 GLU cc_start: 0.8448 (tp30) cc_final: 0.7456 (tp30) REVERT: H 379 ARG cc_start: 0.9172 (tmm-80) cc_final: 0.8321 (tmm-80) REVERT: H 452 MET cc_start: 0.9085 (mmp) cc_final: 0.8433 (mmp) REVERT: H 468 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8565 (mt-10) REVERT: H 485 GLU cc_start: 0.8546 (tp30) cc_final: 0.8297 (tp30) REVERT: H 489 GLN cc_start: 0.8361 (tp40) cc_final: 0.7493 (mt0) REVERT: I 20 GLN cc_start: 0.9134 (mt0) cc_final: 0.8822 (mt0) REVERT: I 40 ASP cc_start: 0.8913 (t0) cc_final: 0.8549 (t0) REVERT: I 51 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: I 206 ASP cc_start: 0.8380 (t0) cc_final: 0.8033 (t0) REVERT: I 207 ASP cc_start: 0.8318 (m-30) cc_final: 0.7530 (m-30) REVERT: I 217 ASP cc_start: 0.8678 (t0) cc_final: 0.8349 (t0) REVERT: I 228 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8625 (mmmm) REVERT: I 245 ASP cc_start: 0.8261 (t70) cc_final: 0.6765 (t0) REVERT: I 376 GLU cc_start: 0.8480 (tp30) cc_final: 0.7470 (tp30) REVERT: I 379 ARG cc_start: 0.9173 (tmm-80) cc_final: 0.8315 (tmm-80) REVERT: I 485 GLU cc_start: 0.8445 (tp30) cc_final: 0.8139 (tp30) REVERT: J 20 GLN cc_start: 0.9052 (mt0) cc_final: 0.8741 (mt0) REVERT: J 40 ASP cc_start: 0.8915 (t0) cc_final: 0.8579 (t0) REVERT: J 105 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8565 (mtpp) REVERT: J 176 ASP cc_start: 0.8278 (m-30) cc_final: 0.8008 (m-30) REVERT: J 217 ASP cc_start: 0.8770 (t0) cc_final: 0.8436 (t0) REVERT: J 228 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8732 (mmmm) REVERT: J 270 MET cc_start: 0.8458 (ttm) cc_final: 0.8163 (ttm) REVERT: J 346 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8434 (p) REVERT: J 376 GLU cc_start: 0.8356 (tp30) cc_final: 0.7710 (tp30) REVERT: J 379 ARG cc_start: 0.9194 (tmm-80) cc_final: 0.8865 (tmm-80) REVERT: J 485 GLU cc_start: 0.8583 (tp30) cc_final: 0.8307 (tp30) REVERT: K 40 ASP cc_start: 0.8855 (t0) cc_final: 0.8438 (t0) REVERT: K 51 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: K 110 ASN cc_start: 0.8914 (m-40) cc_final: 0.8601 (m-40) REVERT: K 217 ASP cc_start: 0.8696 (t0) cc_final: 0.8361 (t0) REVERT: K 228 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8589 (mmmm) REVERT: K 248 LYS cc_start: 0.9001 (mttt) cc_final: 0.8768 (mttt) REVERT: K 346 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8577 (p) REVERT: K 376 GLU cc_start: 0.8442 (tp30) cc_final: 0.7498 (tp30) REVERT: K 379 ARG cc_start: 0.9164 (tmm-80) cc_final: 0.8373 (tmm-80) REVERT: K 426 GLU cc_start: 0.8078 (tt0) cc_final: 0.7851 (tt0) REVERT: K 452 MET cc_start: 0.9103 (mmp) cc_final: 0.8451 (mmp) REVERT: K 458 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8290 (mtp-110) REVERT: K 461 GLU cc_start: 0.7987 (pm20) cc_final: 0.7717 (pm20) REVERT: K 468 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8585 (mt-10) REVERT: L 20 GLN cc_start: 0.9150 (mt0) cc_final: 0.8837 (mt0) REVERT: L 40 ASP cc_start: 0.8921 (t0) cc_final: 0.8552 (t0) REVERT: L 51 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: L 109 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8471 (tpp80) REVERT: L 206 ASP cc_start: 0.8386 (t0) cc_final: 0.8043 (t0) REVERT: L 207 ASP cc_start: 0.8310 (m-30) cc_final: 0.7524 (m-30) REVERT: L 217 ASP cc_start: 0.8645 (t0) cc_final: 0.8309 (t0) REVERT: L 228 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8616 (mmmm) REVERT: L 245 ASP cc_start: 0.8250 (t70) cc_final: 0.6745 (t0) REVERT: L 376 GLU cc_start: 0.8487 (tp30) cc_final: 0.7457 (tp30) REVERT: L 379 ARG cc_start: 0.9175 (tmm-80) cc_final: 0.8286 (tmm-80) REVERT: L 485 GLU cc_start: 0.8505 (tp30) cc_final: 0.8151 (tp30) REVERT: L 487 MET cc_start: 0.9486 (mmm) cc_final: 0.9252 (mtp) outliers start: 196 outliers final: 128 residues processed: 1558 average time/residue: 0.6272 time to fit residues: 1575.9903 Evaluate side-chains 1487 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1349 time to evaluate : 5.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 515 ASP Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 346 SER Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 457 VAL Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 229 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain K residue 448 VAL Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 492 ARG Chi-restraints excluded: chain K residue 508 ASP Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 287 ILE Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 453 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 545 optimal weight: 7.9990 chunk 589 optimal weight: 20.0000 chunk 486 optimal weight: 0.9980 chunk 541 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 437 optimal weight: 30.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN C 504 ASN D 507 ASN ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 HIS E 300 ASN F 507 ASN ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 ASN H 504 ASN I 504 ASN ** J 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 504 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 49392 Z= 0.320 Angle : 0.545 6.251 66708 Z= 0.297 Chirality : 0.042 0.155 7416 Planarity : 0.003 0.044 8496 Dihedral : 7.244 59.845 6700 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.17 % Favored : 96.63 % Rotamer: Outliers : 4.58 % Allowed : 13.60 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.11), residues: 5928 helix: 2.30 (0.09), residues: 2952 sheet: -1.09 (0.15), residues: 984 loop : -0.14 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 307 HIS 0.003 0.001 HIS G 296 PHE 0.022 0.002 PHE E 358 TYR 0.012 0.001 TYR I 381 ARG 0.008 0.000 ARG H 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1590 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 1345 time to evaluate : 6.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9110 (mt0) cc_final: 0.8809 (mt0) REVERT: A 40 ASP cc_start: 0.8938 (t0) cc_final: 0.8564 (t0) REVERT: A 217 ASP cc_start: 0.8731 (t0) cc_final: 0.8398 (t0) REVERT: A 228 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8717 (mmmm) REVERT: A 245 ASP cc_start: 0.8206 (t70) cc_final: 0.7745 (t0) REVERT: A 485 GLU cc_start: 0.8635 (tp30) cc_final: 0.8382 (tp30) REVERT: A 504 ASN cc_start: 0.8321 (m-40) cc_final: 0.8111 (m-40) REVERT: B 40 ASP cc_start: 0.8869 (t0) cc_final: 0.8437 (t0) REVERT: B 217 ASP cc_start: 0.8687 (t0) cc_final: 0.8292 (t0) REVERT: B 228 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8629 (mmmm) REVERT: B 376 GLU cc_start: 0.8464 (tp30) cc_final: 0.7841 (tp30) REVERT: B 379 ARG cc_start: 0.9159 (tmm-80) cc_final: 0.8519 (tmm-80) REVERT: B 452 MET cc_start: 0.9088 (mmp) cc_final: 0.8553 (mmp) REVERT: B 468 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8520 (mt-10) REVERT: B 492 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7445 (ptm160) REVERT: C 20 GLN cc_start: 0.9172 (mt0) cc_final: 0.8865 (mt0) REVERT: C 40 ASP cc_start: 0.8909 (t0) cc_final: 0.8528 (t0) REVERT: C 86 GLU cc_start: 0.6577 (pt0) cc_final: 0.6215 (pt0) REVERT: C 217 ASP cc_start: 0.8643 (t0) cc_final: 0.8289 (t0) REVERT: C 228 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8685 (mmmm) REVERT: C 376 GLU cc_start: 0.8441 (tp30) cc_final: 0.7842 (tp30) REVERT: C 379 ARG cc_start: 0.9174 (tmm-80) cc_final: 0.8610 (tmm-80) REVERT: C 485 GLU cc_start: 0.8569 (tp30) cc_final: 0.8157 (tp30) REVERT: D 20 GLN cc_start: 0.9106 (mt0) cc_final: 0.8767 (mt0) REVERT: D 40 ASP cc_start: 0.8966 (t0) cc_final: 0.8503 (t0) REVERT: D 43 ASP cc_start: 0.9083 (m-30) cc_final: 0.8636 (m-30) REVERT: D 206 ASP cc_start: 0.8396 (t0) cc_final: 0.8129 (t0) REVERT: D 217 ASP cc_start: 0.8733 (t0) cc_final: 0.8369 (t0) REVERT: D 228 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8738 (mmmm) REVERT: D 245 ASP cc_start: 0.8548 (t70) cc_final: 0.7377 (t0) REVERT: D 458 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8229 (mtp-110) REVERT: D 485 GLU cc_start: 0.8705 (tp30) cc_final: 0.8397 (tp30) REVERT: D 516 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8406 (mt-10) REVERT: E 40 ASP cc_start: 0.8868 (t0) cc_final: 0.8441 (t0) REVERT: E 51 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: E 206 ASP cc_start: 0.8431 (t70) cc_final: 0.8051 (t0) REVERT: E 217 ASP cc_start: 0.8699 (t0) cc_final: 0.8311 (t0) REVERT: E 228 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8576 (mmmm) REVERT: E 346 SER cc_start: 0.9069 (m) cc_final: 0.8517 (p) REVERT: E 376 GLU cc_start: 0.8465 (tp30) cc_final: 0.7887 (tp30) REVERT: E 379 ARG cc_start: 0.9157 (tmm-80) cc_final: 0.8546 (tmm-80) REVERT: E 452 MET cc_start: 0.9197 (mmp) cc_final: 0.8810 (mmp) REVERT: E 458 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8331 (mtp-110) REVERT: E 468 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8541 (mt-10) REVERT: F 20 GLN cc_start: 0.9158 (mt0) cc_final: 0.8846 (mt0) REVERT: F 40 ASP cc_start: 0.8911 (t0) cc_final: 0.8539 (t0) REVERT: F 51 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: F 217 ASP cc_start: 0.8653 (t0) cc_final: 0.8361 (t0) REVERT: F 228 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8685 (mmmm) REVERT: F 376 GLU cc_start: 0.8439 (tp30) cc_final: 0.7811 (tp30) REVERT: F 379 ARG cc_start: 0.9175 (tmm-80) cc_final: 0.8621 (tmm-80) REVERT: F 485 GLU cc_start: 0.8586 (tp30) cc_final: 0.8296 (tp30) REVERT: F 516 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8403 (mt-10) REVERT: G 20 GLN cc_start: 0.9067 (mt0) cc_final: 0.8723 (mt0) REVERT: G 40 ASP cc_start: 0.8961 (t0) cc_final: 0.8518 (t0) REVERT: G 43 ASP cc_start: 0.9093 (m-30) cc_final: 0.8677 (m-30) REVERT: G 206 ASP cc_start: 0.8414 (t0) cc_final: 0.8096 (t0) REVERT: G 217 ASP cc_start: 0.8720 (t0) cc_final: 0.8386 (t0) REVERT: G 228 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8791 (mmmm) REVERT: G 245 ASP cc_start: 0.8173 (t70) cc_final: 0.7814 (t0) REVERT: G 376 GLU cc_start: 0.8458 (tp30) cc_final: 0.8242 (tp30) REVERT: G 468 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8651 (mt-10) REVERT: G 485 GLU cc_start: 0.8695 (tp30) cc_final: 0.8411 (tp30) REVERT: G 504 ASN cc_start: 0.8325 (m-40) cc_final: 0.8045 (m-40) REVERT: H 40 ASP cc_start: 0.8866 (t0) cc_final: 0.8420 (t0) REVERT: H 48 ARG cc_start: 0.6747 (tpm170) cc_final: 0.6469 (tpt170) REVERT: H 109 ARG cc_start: 0.8799 (tpp80) cc_final: 0.8525 (tpp80) REVERT: H 217 ASP cc_start: 0.8691 (t0) cc_final: 0.8258 (t0) REVERT: H 228 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8597 (mmmm) REVERT: H 376 GLU cc_start: 0.8474 (tp30) cc_final: 0.7983 (tp30) REVERT: H 379 ARG cc_start: 0.9159 (tmm-80) cc_final: 0.8588 (tmm-80) REVERT: H 452 MET cc_start: 0.9138 (mmp) cc_final: 0.8636 (mmp) REVERT: H 468 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8521 (mt-10) REVERT: H 504 ASN cc_start: 0.8402 (m-40) cc_final: 0.7941 (m110) REVERT: I 20 GLN cc_start: 0.9154 (mt0) cc_final: 0.8852 (mt0) REVERT: I 40 ASP cc_start: 0.8918 (t0) cc_final: 0.8534 (t0) REVERT: I 217 ASP cc_start: 0.8646 (t0) cc_final: 0.8342 (t0) REVERT: I 228 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8689 (mmmm) REVERT: I 376 GLU cc_start: 0.8441 (tp30) cc_final: 0.7827 (tp30) REVERT: I 379 ARG cc_start: 0.9182 (tmm-80) cc_final: 0.8630 (tmm-80) REVERT: I 458 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8364 (ttp80) REVERT: I 468 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8502 (mt-10) REVERT: I 485 GLU cc_start: 0.8487 (tp30) cc_final: 0.8227 (tp30) REVERT: J 20 GLN cc_start: 0.9098 (mt0) cc_final: 0.8780 (mt0) REVERT: J 40 ASP cc_start: 0.8958 (t0) cc_final: 0.8538 (t0) REVERT: J 43 ASP cc_start: 0.9113 (m-30) cc_final: 0.8690 (m-30) REVERT: J 206 ASP cc_start: 0.8420 (t0) cc_final: 0.8155 (t0) REVERT: J 217 ASP cc_start: 0.8735 (t0) cc_final: 0.8393 (t0) REVERT: J 228 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8808 (mmmm) REVERT: J 376 GLU cc_start: 0.8417 (tp30) cc_final: 0.8206 (tp30) REVERT: J 458 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8216 (ttp80) REVERT: J 485 GLU cc_start: 0.8649 (tp30) cc_final: 0.8410 (tp30) REVERT: J 504 ASN cc_start: 0.8268 (m-40) cc_final: 0.7997 (m-40) REVERT: K 40 ASP cc_start: 0.8866 (t0) cc_final: 0.8440 (t0) REVERT: K 51 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: K 217 ASP cc_start: 0.8688 (t0) cc_final: 0.8293 (t0) REVERT: K 228 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8626 (mmmm) REVERT: K 376 GLU cc_start: 0.8453 (tp30) cc_final: 0.7977 (tp30) REVERT: K 379 ARG cc_start: 0.9156 (tmm-80) cc_final: 0.8584 (tmm-80) REVERT: K 452 MET cc_start: 0.9117 (mmp) cc_final: 0.8566 (mmp) REVERT: K 458 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8315 (mtp-110) REVERT: K 468 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8533 (mt-10) REVERT: L 20 GLN cc_start: 0.9168 (mt0) cc_final: 0.8843 (mt0) REVERT: L 40 ASP cc_start: 0.8913 (t0) cc_final: 0.8531 (t0) REVERT: L 51 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: L 217 ASP cc_start: 0.8641 (t0) cc_final: 0.8289 (t0) REVERT: L 228 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8685 (mmmm) REVERT: L 376 GLU cc_start: 0.8428 (tp30) cc_final: 0.7799 (tp30) REVERT: L 379 ARG cc_start: 0.9194 (tmm-80) cc_final: 0.8457 (tmm-80) REVERT: L 468 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8524 (mt-10) REVERT: L 485 GLU cc_start: 0.8522 (tp30) cc_final: 0.8202 (tp30) REVERT: L 522 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8517 (ptmm) outliers start: 245 outliers final: 176 residues processed: 1473 average time/residue: 0.6855 time to fit residues: 1638.7065 Evaluate side-chains 1465 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1284 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 492 ARG Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 457 VAL Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 515 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 229 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 508 ASP Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 57 LYS Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 227 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 8.9990 chunk 410 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 260 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 547 optimal weight: 10.0000 chunk 579 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 519 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 HIS B 300 ASN C 504 ASN C 507 ASN E 300 ASN F 504 ASN F 526 ASN H 300 ASN H 489 GLN I 296 HIS I 507 ASN J 296 HIS ** J 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 507 ASN ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 507 ASN L 507 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 49392 Z= 0.239 Angle : 0.517 7.332 66708 Z= 0.282 Chirality : 0.042 0.225 7416 Planarity : 0.003 0.056 8496 Dihedral : 6.915 59.681 6680 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.02 % Favored : 96.78 % Rotamer: Outliers : 4.28 % Allowed : 14.99 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.11), residues: 5928 helix: 2.40 (0.09), residues: 2904 sheet: -0.99 (0.16), residues: 984 loop : 0.03 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 307 HIS 0.002 0.001 HIS J 433 PHE 0.016 0.001 PHE K 256 TYR 0.012 0.001 TYR E 381 ARG 0.010 0.000 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1594 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 1365 time to evaluate : 5.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9094 (mt0) cc_final: 0.8757 (mt0) REVERT: A 40 ASP cc_start: 0.8938 (t0) cc_final: 0.8477 (t0) REVERT: A 43 ASP cc_start: 0.9106 (m-30) cc_final: 0.8641 (m-30) REVERT: A 206 ASP cc_start: 0.8226 (t0) cc_final: 0.7987 (t0) REVERT: A 207 ASP cc_start: 0.8200 (m-30) cc_final: 0.7904 (m-30) REVERT: A 217 ASP cc_start: 0.8741 (t0) cc_final: 0.8411 (t0) REVERT: A 228 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8664 (mmmm) REVERT: A 485 GLU cc_start: 0.8618 (tp30) cc_final: 0.8355 (tp30) REVERT: A 504 ASN cc_start: 0.8333 (m-40) cc_final: 0.8108 (m-40) REVERT: B 40 ASP cc_start: 0.8879 (t0) cc_final: 0.8432 (t0) REVERT: B 86 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6737 (pt0) REVERT: B 217 ASP cc_start: 0.8693 (t0) cc_final: 0.8294 (t0) REVERT: B 228 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8603 (mmmm) REVERT: B 245 ASP cc_start: 0.8465 (t70) cc_final: 0.6773 (t70) REVERT: B 248 LYS cc_start: 0.9018 (mttt) cc_final: 0.8816 (mttt) REVERT: B 376 GLU cc_start: 0.8448 (tp30) cc_final: 0.7959 (tp30) REVERT: B 379 ARG cc_start: 0.9142 (tmm-80) cc_final: 0.8624 (tmm-80) REVERT: B 452 MET cc_start: 0.9051 (mmp) cc_final: 0.8531 (mmp) REVERT: B 468 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 492 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7399 (ptm160) REVERT: C 20 GLN cc_start: 0.9165 (mt0) cc_final: 0.8855 (mt0) REVERT: C 40 ASP cc_start: 0.8904 (t0) cc_final: 0.8537 (t0) REVERT: C 51 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7224 (pm20) REVERT: C 206 ASP cc_start: 0.8362 (t0) cc_final: 0.7916 (t0) REVERT: C 207 ASP cc_start: 0.8242 (m-30) cc_final: 0.7645 (m-30) REVERT: C 217 ASP cc_start: 0.8659 (t0) cc_final: 0.8303 (t0) REVERT: C 228 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8641 (mmmm) REVERT: C 376 GLU cc_start: 0.8426 (tp30) cc_final: 0.7936 (tp30) REVERT: C 379 ARG cc_start: 0.9139 (tmm-80) cc_final: 0.8557 (tmm-80) REVERT: D 20 GLN cc_start: 0.9089 (mt0) cc_final: 0.8573 (mt0) REVERT: D 40 ASP cc_start: 0.8962 (t0) cc_final: 0.8466 (t0) REVERT: D 43 ASP cc_start: 0.9085 (m-30) cc_final: 0.8627 (m-30) REVERT: D 217 ASP cc_start: 0.8724 (t0) cc_final: 0.8373 (t0) REVERT: D 228 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8661 (mmmm) REVERT: D 245 ASP cc_start: 0.8192 (t70) cc_final: 0.7809 (t0) REVERT: D 246 LYS cc_start: 0.9155 (mttp) cc_final: 0.8947 (mttp) REVERT: D 248 LYS cc_start: 0.8804 (mttt) cc_final: 0.8576 (mttt) REVERT: D 458 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8284 (mtp-110) REVERT: D 461 GLU cc_start: 0.8275 (pm20) cc_final: 0.7850 (pm20) REVERT: D 485 GLU cc_start: 0.8672 (tp30) cc_final: 0.8314 (tp30) REVERT: D 504 ASN cc_start: 0.8339 (m-40) cc_final: 0.8109 (m-40) REVERT: E 40 ASP cc_start: 0.8880 (t0) cc_final: 0.8302 (t0) REVERT: E 43 ASP cc_start: 0.9101 (m-30) cc_final: 0.8510 (m-30) REVERT: E 51 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: E 206 ASP cc_start: 0.8401 (t70) cc_final: 0.8063 (t0) REVERT: E 217 ASP cc_start: 0.8696 (t0) cc_final: 0.8338 (t0) REVERT: E 228 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8588 (mmmm) REVERT: E 346 SER cc_start: 0.9071 (m) cc_final: 0.8544 (p) REVERT: E 376 GLU cc_start: 0.8454 (tp30) cc_final: 0.7489 (tp30) REVERT: E 379 ARG cc_start: 0.9131 (tmm-80) cc_final: 0.8288 (tmm-80) REVERT: E 426 GLU cc_start: 0.8108 (tt0) cc_final: 0.7897 (tt0) REVERT: E 452 MET cc_start: 0.9122 (mmp) cc_final: 0.8779 (mmp) REVERT: E 461 GLU cc_start: 0.8127 (pm20) cc_final: 0.7850 (pm20) REVERT: E 468 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8542 (mt-10) REVERT: F 1 MET cc_start: 0.8284 (ppp) cc_final: 0.8041 (ppp) REVERT: F 20 GLN cc_start: 0.9164 (mt0) cc_final: 0.8836 (mt0) REVERT: F 40 ASP cc_start: 0.8910 (t0) cc_final: 0.8539 (t0) REVERT: F 51 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: F 206 ASP cc_start: 0.8248 (t0) cc_final: 0.7884 (t0) REVERT: F 207 ASP cc_start: 0.8185 (m-30) cc_final: 0.7667 (m-30) REVERT: F 217 ASP cc_start: 0.8667 (t0) cc_final: 0.8353 (t0) REVERT: F 228 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8644 (mmmm) REVERT: F 376 GLU cc_start: 0.8452 (tp30) cc_final: 0.7966 (tp30) REVERT: F 379 ARG cc_start: 0.9138 (tmm-80) cc_final: 0.8582 (tmm-80) REVERT: F 485 GLU cc_start: 0.8582 (tp30) cc_final: 0.8308 (tp30) REVERT: F 522 LYS cc_start: 0.9106 (tmtt) cc_final: 0.8843 (tmtt) REVERT: F 523 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9056 (ptpp) REVERT: G 20 GLN cc_start: 0.9073 (mt0) cc_final: 0.8691 (mt0) REVERT: G 40 ASP cc_start: 0.8970 (t0) cc_final: 0.8488 (t0) REVERT: G 43 ASP cc_start: 0.9095 (m-30) cc_final: 0.8618 (m-30) REVERT: G 217 ASP cc_start: 0.8739 (t0) cc_final: 0.8380 (t0) REVERT: G 468 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8621 (mt-10) REVERT: G 485 GLU cc_start: 0.8664 (tp30) cc_final: 0.8360 (tp30) REVERT: G 504 ASN cc_start: 0.8275 (m-40) cc_final: 0.7958 (m-40) REVERT: H 40 ASP cc_start: 0.8875 (t0) cc_final: 0.8426 (t0) REVERT: H 217 ASP cc_start: 0.8689 (t0) cc_final: 0.8335 (t0) REVERT: H 228 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8577 (mmmm) REVERT: H 376 GLU cc_start: 0.8458 (tp30) cc_final: 0.8162 (tp30) REVERT: H 379 ARG cc_start: 0.9124 (tmm-80) cc_final: 0.8628 (tmm-80) REVERT: H 452 MET cc_start: 0.9058 (mmp) cc_final: 0.8850 (mmp) REVERT: H 468 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8530 (mt-10) REVERT: H 485 GLU cc_start: 0.8590 (tp30) cc_final: 0.8355 (tp30) REVERT: I 20 GLN cc_start: 0.9163 (mt0) cc_final: 0.8793 (mt0) REVERT: I 40 ASP cc_start: 0.8909 (t0) cc_final: 0.8315 (t0) REVERT: I 43 ASP cc_start: 0.9108 (m-30) cc_final: 0.8324 (m-30) REVERT: I 51 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: I 206 ASP cc_start: 0.8351 (t0) cc_final: 0.7865 (t0) REVERT: I 207 ASP cc_start: 0.8312 (m-30) cc_final: 0.7783 (m-30) REVERT: I 217 ASP cc_start: 0.8659 (t0) cc_final: 0.8360 (t0) REVERT: I 228 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8632 (mmmm) REVERT: I 376 GLU cc_start: 0.8436 (tp30) cc_final: 0.7901 (tp30) REVERT: I 379 ARG cc_start: 0.9141 (tmm-80) cc_final: 0.8557 (tmm-80) REVERT: I 458 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8328 (ttp80) REVERT: I 461 GLU cc_start: 0.8256 (pm20) cc_final: 0.7935 (pm20) REVERT: I 468 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8410 (mt-10) REVERT: I 485 GLU cc_start: 0.8500 (tp30) cc_final: 0.8222 (tp30) REVERT: I 487 MET cc_start: 0.9475 (mmm) cc_final: 0.9275 (mtp) REVERT: J 1 MET cc_start: 0.8117 (ppp) cc_final: 0.7872 (tmm) REVERT: J 20 GLN cc_start: 0.9081 (mt0) cc_final: 0.8704 (mt0) REVERT: J 40 ASP cc_start: 0.8955 (t0) cc_final: 0.8509 (t0) REVERT: J 43 ASP cc_start: 0.9108 (m-30) cc_final: 0.8676 (m-30) REVERT: J 206 ASP cc_start: 0.8325 (t0) cc_final: 0.8119 (t0) REVERT: J 217 ASP cc_start: 0.8759 (t0) cc_final: 0.8409 (t0) REVERT: J 228 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8765 (mmmm) REVERT: J 485 GLU cc_start: 0.8605 (tp30) cc_final: 0.8274 (tp30) REVERT: J 504 ASN cc_start: 0.8294 (m-40) cc_final: 0.7985 (m-40) REVERT: K 40 ASP cc_start: 0.8879 (t0) cc_final: 0.8435 (t0) REVERT: K 51 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: K 217 ASP cc_start: 0.8677 (t0) cc_final: 0.8293 (t0) REVERT: K 228 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8605 (mmmm) REVERT: K 245 ASP cc_start: 0.8462 (t70) cc_final: 0.6758 (t70) REVERT: K 248 LYS cc_start: 0.9018 (mttt) cc_final: 0.8818 (mttt) REVERT: K 346 SER cc_start: 0.9019 (m) cc_final: 0.8446 (p) REVERT: K 376 GLU cc_start: 0.8429 (tp30) cc_final: 0.7428 (tp30) REVERT: K 377 ARG cc_start: 0.9291 (ptm-80) cc_final: 0.8862 (ptm-80) REVERT: K 379 ARG cc_start: 0.9129 (tmm-80) cc_final: 0.8273 (tmm-80) REVERT: K 426 GLU cc_start: 0.8092 (tt0) cc_final: 0.7874 (tt0) REVERT: K 452 MET cc_start: 0.9039 (mmp) cc_final: 0.8445 (mmp) REVERT: K 458 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8314 (mtp-110) REVERT: K 468 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8558 (mt-10) REVERT: L 20 GLN cc_start: 0.9161 (mt0) cc_final: 0.8834 (mt0) REVERT: L 40 ASP cc_start: 0.8909 (t0) cc_final: 0.8537 (t0) REVERT: L 51 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: L 217 ASP cc_start: 0.8659 (t0) cc_final: 0.8304 (t0) REVERT: L 228 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8640 (mmmm) REVERT: L 376 GLU cc_start: 0.8426 (tp30) cc_final: 0.7893 (tp30) REVERT: L 379 ARG cc_start: 0.9146 (tmm-80) cc_final: 0.8552 (tmm-80) REVERT: L 458 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8299 (ttp80) REVERT: L 461 GLU cc_start: 0.8328 (pm20) cc_final: 0.8031 (pm20) REVERT: L 468 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8499 (mt-10) REVERT: L 485 GLU cc_start: 0.8519 (tp30) cc_final: 0.8189 (tp30) outliers start: 229 outliers final: 180 residues processed: 1486 average time/residue: 0.6252 time to fit residues: 1502.6812 Evaluate side-chains 1491 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1302 time to evaluate : 5.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 LYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 489 GLN Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 515 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 229 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 508 ASP Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain K residue 518 LEU Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 227 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 431 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 494 optimal weight: 1.9990 chunk 400 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 520 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN C 296 HIS C 300 ASN D 296 HIS ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 ASN E 526 ASN F 296 HIS H 489 GLN H 504 ASN I 507 ASN I 526 ASN J 76 GLN ** J 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 507 ASN ** K 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 HIS L 507 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 49392 Z= 0.330 Angle : 0.564 7.819 66708 Z= 0.306 Chirality : 0.043 0.240 7416 Planarity : 0.003 0.068 8496 Dihedral : 6.912 59.761 6676 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.05 % Favored : 96.74 % Rotamer: Outliers : 4.78 % Allowed : 15.71 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.11), residues: 5928 helix: 2.22 (0.09), residues: 2952 sheet: -0.95 (0.16), residues: 984 loop : -0.17 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 307 HIS 0.002 0.001 HIS K 433 PHE 0.023 0.002 PHE E 161 TYR 0.012 0.001 TYR L 381 ARG 0.010 0.000 ARG C 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1584 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 1328 time to evaluate : 5.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7828 (tmm) REVERT: A 20 GLN cc_start: 0.9150 (mt0) cc_final: 0.8793 (mt0) REVERT: A 40 ASP cc_start: 0.8952 (t0) cc_final: 0.8459 (t0) REVERT: A 217 ASP cc_start: 0.8735 (t0) cc_final: 0.8390 (t0) REVERT: A 228 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8713 (mmmm) REVERT: A 458 ARG cc_start: 0.8632 (mtm110) cc_final: 0.8327 (ttp80) REVERT: A 485 GLU cc_start: 0.8635 (tp30) cc_final: 0.8347 (tp30) REVERT: A 523 LYS cc_start: 0.9183 (ptpp) cc_final: 0.8897 (pttm) REVERT: B 40 ASP cc_start: 0.8892 (t0) cc_final: 0.8313 (t0) REVERT: B 43 ASP cc_start: 0.9132 (m-30) cc_final: 0.8550 (m-30) REVERT: B 217 ASP cc_start: 0.8679 (t0) cc_final: 0.8286 (t0) REVERT: B 228 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8618 (mmmm) REVERT: B 290 LEU cc_start: 0.9748 (mt) cc_final: 0.9529 (mt) REVERT: B 376 GLU cc_start: 0.8433 (tp30) cc_final: 0.8150 (tp30) REVERT: B 379 ARG cc_start: 0.9132 (tmm-80) cc_final: 0.8643 (tmm-80) REVERT: B 452 MET cc_start: 0.8999 (mmp) cc_final: 0.8452 (mmp) REVERT: B 455 TYR cc_start: 0.7787 (m-80) cc_final: 0.6660 (m-80) REVERT: B 458 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8318 (ttp80) REVERT: B 468 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8555 (mt-10) REVERT: C 20 GLN cc_start: 0.9187 (mt0) cc_final: 0.8854 (mt0) REVERT: C 40 ASP cc_start: 0.8925 (t0) cc_final: 0.8562 (t0) REVERT: C 51 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: C 206 ASP cc_start: 0.8436 (t0) cc_final: 0.8182 (t0) REVERT: C 217 ASP cc_start: 0.8635 (t0) cc_final: 0.8261 (t0) REVERT: C 228 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8633 (mmmm) REVERT: C 350 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6485 (mm-30) REVERT: C 376 GLU cc_start: 0.8404 (tp30) cc_final: 0.7342 (tp30) REVERT: C 379 ARG cc_start: 0.9141 (tmm-80) cc_final: 0.8177 (tmm-80) REVERT: C 461 GLU cc_start: 0.8280 (pm20) cc_final: 0.7983 (pm20) REVERT: D 20 GLN cc_start: 0.9135 (mt0) cc_final: 0.8759 (mt0) REVERT: D 40 ASP cc_start: 0.8970 (t0) cc_final: 0.8480 (t0) REVERT: D 48 ARG cc_start: 0.6771 (tpt170) cc_final: 0.6373 (tpt170) REVERT: D 217 ASP cc_start: 0.8735 (t0) cc_final: 0.8383 (t0) REVERT: D 228 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8624 (mmmm) REVERT: D 245 ASP cc_start: 0.8270 (t70) cc_final: 0.7816 (t0) REVERT: D 246 LYS cc_start: 0.9159 (mttp) cc_final: 0.8936 (mttp) REVERT: D 379 ARG cc_start: 0.9098 (tmm-80) cc_final: 0.8783 (tmm-80) REVERT: D 458 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8261 (mtp-110) REVERT: D 485 GLU cc_start: 0.8711 (tp30) cc_final: 0.8379 (tp30) REVERT: D 504 ASN cc_start: 0.8356 (m-40) cc_final: 0.8107 (m-40) REVERT: E 40 ASP cc_start: 0.8896 (t0) cc_final: 0.8323 (t0) REVERT: E 43 ASP cc_start: 0.9111 (m-30) cc_final: 0.8524 (m-30) REVERT: E 206 ASP cc_start: 0.8461 (t70) cc_final: 0.8126 (t0) REVERT: E 217 ASP cc_start: 0.8687 (t0) cc_final: 0.8289 (t0) REVERT: E 228 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8591 (mmmm) REVERT: E 346 SER cc_start: 0.9087 (m) cc_final: 0.8510 (p) REVERT: E 376 GLU cc_start: 0.8433 (tp30) cc_final: 0.8110 (tp30) REVERT: E 377 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8829 (ttm-80) REVERT: E 379 ARG cc_start: 0.9131 (tmm-80) cc_final: 0.8626 (tmm-80) REVERT: E 452 MET cc_start: 0.9131 (mmp) cc_final: 0.8541 (mmp) REVERT: E 468 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8516 (mt-10) REVERT: F 20 GLN cc_start: 0.9185 (mt0) cc_final: 0.8865 (mt0) REVERT: F 40 ASP cc_start: 0.8927 (t0) cc_final: 0.8565 (t0) REVERT: F 51 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: F 217 ASP cc_start: 0.8649 (t0) cc_final: 0.8346 (t0) REVERT: F 228 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8632 (mmmm) REVERT: F 376 GLU cc_start: 0.8403 (tp30) cc_final: 0.7959 (tp30) REVERT: F 379 ARG cc_start: 0.9143 (tmm-80) cc_final: 0.8615 (tmm-80) REVERT: F 522 LYS cc_start: 0.9059 (tmtt) cc_final: 0.8791 (tmtt) REVERT: F 523 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9073 (ptpp) REVERT: G 20 GLN cc_start: 0.9131 (mt0) cc_final: 0.8702 (mt0) REVERT: G 40 ASP cc_start: 0.8984 (t0) cc_final: 0.8501 (t0) REVERT: G 217 ASP cc_start: 0.8709 (t0) cc_final: 0.8351 (t0) REVERT: G 228 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8708 (mmmm) REVERT: G 376 GLU cc_start: 0.8379 (tp30) cc_final: 0.7351 (tp30) REVERT: G 379 ARG cc_start: 0.9233 (tmm-80) cc_final: 0.8926 (tmm-80) REVERT: G 468 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8590 (mt-10) REVERT: G 485 GLU cc_start: 0.8680 (tp30) cc_final: 0.8417 (tp30) REVERT: G 504 ASN cc_start: 0.8310 (m-40) cc_final: 0.7985 (m-40) REVERT: H 40 ASP cc_start: 0.8884 (t0) cc_final: 0.8308 (t0) REVERT: H 43 ASP cc_start: 0.9131 (m-30) cc_final: 0.8540 (m-30) REVERT: H 217 ASP cc_start: 0.8681 (t0) cc_final: 0.8243 (t0) REVERT: H 228 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8585 (mmmm) REVERT: H 346 SER cc_start: 0.8969 (m) cc_final: 0.8328 (p) REVERT: H 376 GLU cc_start: 0.8440 (tp30) cc_final: 0.8159 (tp30) REVERT: H 377 ARG cc_start: 0.9244 (ptm-80) cc_final: 0.8913 (ptm-80) REVERT: H 379 ARG cc_start: 0.9135 (tmm-80) cc_final: 0.8649 (tmm-80) REVERT: H 452 MET cc_start: 0.9086 (mmp) cc_final: 0.8825 (mmp) REVERT: H 455 TYR cc_start: 0.7860 (m-80) cc_final: 0.7052 (m-80) REVERT: H 458 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8314 (ttp80) REVERT: H 468 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8539 (mt-10) REVERT: I 20 GLN cc_start: 0.9186 (mt0) cc_final: 0.8872 (mt0) REVERT: I 40 ASP cc_start: 0.8930 (t0) cc_final: 0.8567 (t0) REVERT: I 51 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: I 206 ASP cc_start: 0.8449 (t0) cc_final: 0.8202 (t0) REVERT: I 217 ASP cc_start: 0.8634 (t0) cc_final: 0.8325 (t0) REVERT: I 228 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8631 (mmmm) REVERT: I 376 GLU cc_start: 0.8414 (tp30) cc_final: 0.7349 (tp30) REVERT: I 379 ARG cc_start: 0.9152 (tmm-80) cc_final: 0.8194 (tmm-80) REVERT: I 468 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8368 (mt-10) REVERT: I 485 GLU cc_start: 0.8475 (tp30) cc_final: 0.8234 (tp30) REVERT: I 487 MET cc_start: 0.9493 (mmm) cc_final: 0.9267 (mtp) REVERT: I 492 ARG cc_start: 0.8077 (ptp-110) cc_final: 0.7853 (ptm160) REVERT: J 20 GLN cc_start: 0.9110 (mt0) cc_final: 0.8761 (mt0) REVERT: J 40 ASP cc_start: 0.8972 (t0) cc_final: 0.8502 (t0) REVERT: J 105 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8656 (ttmm) REVERT: J 206 ASP cc_start: 0.8376 (t0) cc_final: 0.8153 (t0) REVERT: J 217 ASP cc_start: 0.8738 (t0) cc_final: 0.8384 (t0) REVERT: J 228 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8731 (mmmm) REVERT: J 346 SER cc_start: 0.9115 (m) cc_final: 0.8567 (p) REVERT: J 458 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8067 (mtp-110) REVERT: J 461 GLU cc_start: 0.8156 (pm20) cc_final: 0.7812 (pm20) REVERT: J 485 GLU cc_start: 0.8645 (tp30) cc_final: 0.8336 (tp30) REVERT: J 489 GLN cc_start: 0.8134 (tp-100) cc_final: 0.7833 (tp40) REVERT: J 492 ARG cc_start: 0.8274 (ptp-170) cc_final: 0.7862 (ptp-170) REVERT: J 504 ASN cc_start: 0.8331 (m-40) cc_final: 0.8075 (m-40) REVERT: K 40 ASP cc_start: 0.8888 (t0) cc_final: 0.8314 (t0) REVERT: K 43 ASP cc_start: 0.9133 (m-30) cc_final: 0.8548 (m-30) REVERT: K 217 ASP cc_start: 0.8680 (t0) cc_final: 0.8284 (t0) REVERT: K 228 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8616 (mmmm) REVERT: K 346 SER cc_start: 0.9096 (m) cc_final: 0.8470 (p) REVERT: K 376 GLU cc_start: 0.8424 (tp30) cc_final: 0.8170 (tp30) REVERT: K 377 ARG cc_start: 0.9318 (ptm-80) cc_final: 0.9081 (ptm-80) REVERT: K 379 ARG cc_start: 0.9132 (tmm-80) cc_final: 0.8658 (tmm-80) REVERT: K 452 MET cc_start: 0.9055 (mmp) cc_final: 0.8505 (mmp) REVERT: K 458 ARG cc_start: 0.8592 (ttp80) cc_final: 0.8310 (mtp-110) REVERT: K 468 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8485 (mt-10) REVERT: L 20 GLN cc_start: 0.9182 (mt0) cc_final: 0.8851 (mt0) REVERT: L 40 ASP cc_start: 0.8929 (t0) cc_final: 0.8566 (t0) REVERT: L 51 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: L 217 ASP cc_start: 0.8635 (t0) cc_final: 0.8258 (t0) REVERT: L 228 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8631 (mmmm) REVERT: L 376 GLU cc_start: 0.8411 (tp30) cc_final: 0.7335 (tp30) REVERT: L 379 ARG cc_start: 0.9141 (tmm-80) cc_final: 0.8165 (tmm-80) REVERT: L 458 ARG cc_start: 0.8561 (ttp80) cc_final: 0.8345 (ttp80) REVERT: L 461 GLU cc_start: 0.8441 (pm20) cc_final: 0.8148 (pm20) REVERT: L 468 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8398 (mt-10) REVERT: L 492 ARG cc_start: 0.8012 (ptp-110) cc_final: 0.7788 (ptm160) REVERT: L 522 LYS cc_start: 0.8960 (ttpp) cc_final: 0.8403 (ptmm) REVERT: L 523 LYS cc_start: 0.9233 (ptpp) cc_final: 0.8988 (ptpp) outliers start: 256 outliers final: 214 residues processed: 1465 average time/residue: 0.6612 time to fit residues: 1575.1740 Evaluate side-chains 1486 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 1265 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 LYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 393 PHE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 489 GLN Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 377 ARG Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 457 VAL Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 515 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 229 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 508 ASP Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 227 SER Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 270 MET Chi-restraints excluded: chain L residue 308 ILE Chi-restraints excluded: chain L residue 377 ARG Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 4.9990 chunk 522 optimal weight: 9.9990 chunk 114 optimal weight: 0.0570 chunk 340 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 580 optimal weight: 2.9990 chunk 481 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 304 optimal weight: 0.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS A 507 ASN E 504 ASN ** G 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 489 GLN K 296 HIS K 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 49392 Z= 0.177 Angle : 0.531 8.580 66708 Z= 0.286 Chirality : 0.042 0.244 7416 Planarity : 0.003 0.054 8496 Dihedral : 6.595 59.796 6660 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.06 % Rotamer: Outliers : 4.56 % Allowed : 16.31 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.11), residues: 5928 helix: 2.34 (0.09), residues: 2904 sheet: -0.83 (0.16), residues: 984 loop : 0.08 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 307 HIS 0.001 0.000 HIS J 296 PHE 0.014 0.001 PHE H 161 TYR 0.011 0.001 TYR L 381 ARG 0.014 0.001 ARG C 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 1387 time to evaluate : 5.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8015 (tmm) REVERT: A 20 GLN cc_start: 0.9087 (mt0) cc_final: 0.8635 (mt0) REVERT: A 40 ASP cc_start: 0.8955 (t0) cc_final: 0.8466 (t0) REVERT: A 207 ASP cc_start: 0.8204 (m-30) cc_final: 0.8004 (m-30) REVERT: A 217 ASP cc_start: 0.8728 (t0) cc_final: 0.8379 (t0) REVERT: A 228 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8626 (mmmm) REVERT: A 458 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8266 (ttp80) REVERT: A 461 GLU cc_start: 0.8256 (pm20) cc_final: 0.7971 (pm20) REVERT: B 40 ASP cc_start: 0.8871 (t0) cc_final: 0.8242 (t0) REVERT: B 43 ASP cc_start: 0.9097 (m-30) cc_final: 0.8533 (m-30) REVERT: B 217 ASP cc_start: 0.8661 (t0) cc_final: 0.8327 (t0) REVERT: B 228 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8542 (mmmm) REVERT: B 376 GLU cc_start: 0.8376 (tp30) cc_final: 0.7941 (tp30) REVERT: B 377 ARG cc_start: 0.9216 (ptm-80) cc_final: 0.8910 (ptm-80) REVERT: B 379 ARG cc_start: 0.9116 (tmm-80) cc_final: 0.8856 (tmm-80) REVERT: B 426 GLU cc_start: 0.8090 (tt0) cc_final: 0.7853 (tt0) REVERT: B 452 MET cc_start: 0.8922 (mmp) cc_final: 0.8482 (mmp) REVERT: B 468 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8621 (mt-10) REVERT: C 20 GLN cc_start: 0.9165 (mt0) cc_final: 0.8844 (mt0) REVERT: C 40 ASP cc_start: 0.8903 (t0) cc_final: 0.8490 (t0) REVERT: C 206 ASP cc_start: 0.8374 (t0) cc_final: 0.8076 (t0) REVERT: C 207 ASP cc_start: 0.8230 (m-30) cc_final: 0.7545 (m-30) REVERT: C 217 ASP cc_start: 0.8675 (t0) cc_final: 0.8314 (t0) REVERT: C 228 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8592 (mmmm) REVERT: C 350 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6317 (mm-30) REVERT: C 376 GLU cc_start: 0.8418 (tp30) cc_final: 0.7959 (tp30) REVERT: C 379 ARG cc_start: 0.9108 (tmm-80) cc_final: 0.8618 (tmm-80) REVERT: C 452 MET cc_start: 0.8972 (mmp) cc_final: 0.8608 (mmp) REVERT: D 20 GLN cc_start: 0.9089 (mt0) cc_final: 0.8580 (mt0) REVERT: D 40 ASP cc_start: 0.8949 (t0) cc_final: 0.8431 (t0) REVERT: D 217 ASP cc_start: 0.8728 (t0) cc_final: 0.8369 (t0) REVERT: D 228 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8558 (mmmm) REVERT: D 246 LYS cc_start: 0.9177 (mttp) cc_final: 0.8957 (mttp) REVERT: D 458 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8256 (mtp-110) REVERT: D 485 GLU cc_start: 0.8662 (tp30) cc_final: 0.8364 (tp30) REVERT: D 504 ASN cc_start: 0.8398 (m-40) cc_final: 0.8089 (m-40) REVERT: E 40 ASP cc_start: 0.8865 (t0) cc_final: 0.8235 (t0) REVERT: E 43 ASP cc_start: 0.9093 (m-30) cc_final: 0.8531 (m-30) REVERT: E 157 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7956 (mmtt) REVERT: E 206 ASP cc_start: 0.8387 (t70) cc_final: 0.8013 (t0) REVERT: E 217 ASP cc_start: 0.8667 (t0) cc_final: 0.8328 (t0) REVERT: E 228 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8560 (mmmm) REVERT: E 346 SER cc_start: 0.9105 (m) cc_final: 0.8552 (p) REVERT: E 376 GLU cc_start: 0.8402 (tp30) cc_final: 0.7990 (tp30) REVERT: E 379 ARG cc_start: 0.9108 (tmm-80) cc_final: 0.8845 (tmm-80) REVERT: E 452 MET cc_start: 0.8998 (mmp) cc_final: 0.8791 (mmp) REVERT: E 458 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8290 (ttp80) REVERT: E 461 GLU cc_start: 0.8061 (pm20) cc_final: 0.7677 (pm20) REVERT: E 468 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8566 (mt-10) REVERT: E 501 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7951 (tm-30) REVERT: F 1 MET cc_start: 0.8270 (ppp) cc_final: 0.7944 (ppp) REVERT: F 20 GLN cc_start: 0.9172 (mt0) cc_final: 0.8853 (mt0) REVERT: F 40 ASP cc_start: 0.8907 (t0) cc_final: 0.8439 (t0) REVERT: F 51 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: F 206 ASP cc_start: 0.8284 (t0) cc_final: 0.7923 (t0) REVERT: F 207 ASP cc_start: 0.8149 (m-30) cc_final: 0.7685 (m-30) REVERT: F 217 ASP cc_start: 0.8650 (t0) cc_final: 0.8287 (t0) REVERT: F 228 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8614 (mmmm) REVERT: F 376 GLU cc_start: 0.8421 (tp30) cc_final: 0.7982 (tp30) REVERT: F 379 ARG cc_start: 0.9117 (tmm-80) cc_final: 0.8649 (tmm-80) REVERT: F 485 GLU cc_start: 0.8559 (tp30) cc_final: 0.8292 (tp30) REVERT: F 522 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8826 (tmtt) REVERT: F 523 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9047 (ptpp) REVERT: G 20 GLN cc_start: 0.9074 (mt0) cc_final: 0.8540 (mt0) REVERT: G 40 ASP cc_start: 0.8962 (t0) cc_final: 0.8461 (t0) REVERT: G 217 ASP cc_start: 0.8740 (t0) cc_final: 0.8373 (t0) REVERT: G 376 GLU cc_start: 0.8371 (tp30) cc_final: 0.7261 (tp30) REVERT: G 379 ARG cc_start: 0.9170 (tmm-80) cc_final: 0.8938 (tmm-80) REVERT: G 426 GLU cc_start: 0.8162 (tt0) cc_final: 0.7879 (tt0) REVERT: G 458 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8143 (mtm-85) REVERT: G 468 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8653 (mt-10) REVERT: G 485 GLU cc_start: 0.8655 (tp30) cc_final: 0.8367 (tp30) REVERT: G 492 ARG cc_start: 0.8082 (ptm160) cc_final: 0.7120 (ptp90) REVERT: G 504 ASN cc_start: 0.8383 (m-40) cc_final: 0.8030 (m-40) REVERT: G 523 LYS cc_start: 0.9153 (ptpp) cc_final: 0.8906 (ptpp) REVERT: H 1 MET cc_start: 0.7982 (ppp) cc_final: 0.7758 (ppp) REVERT: H 40 ASP cc_start: 0.8867 (t0) cc_final: 0.8219 (t0) REVERT: H 43 ASP cc_start: 0.9099 (m-30) cc_final: 0.8529 (m-30) REVERT: H 217 ASP cc_start: 0.8661 (t0) cc_final: 0.8284 (t0) REVERT: H 228 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8554 (mmmm) REVERT: H 346 SER cc_start: 0.8973 (m) cc_final: 0.8350 (p) REVERT: H 376 GLU cc_start: 0.8390 (tp30) cc_final: 0.7282 (tp30) REVERT: H 377 ARG cc_start: 0.9229 (ptm-80) cc_final: 0.8943 (ptm-80) REVERT: H 379 ARG cc_start: 0.9114 (tmm-80) cc_final: 0.8712 (tmm-80) REVERT: H 468 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8612 (mt-10) REVERT: H 504 ASN cc_start: 0.8415 (m-40) cc_final: 0.8183 (m110) REVERT: I 20 GLN cc_start: 0.9161 (mt0) cc_final: 0.8774 (mt0) REVERT: I 40 ASP cc_start: 0.8900 (t0) cc_final: 0.8229 (t0) REVERT: I 43 ASP cc_start: 0.9083 (m-30) cc_final: 0.8457 (m-30) REVERT: I 48 ARG cc_start: 0.6383 (tpt170) cc_final: 0.5921 (tpt170) REVERT: I 51 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: I 206 ASP cc_start: 0.8387 (t0) cc_final: 0.8032 (t0) REVERT: I 207 ASP cc_start: 0.8233 (m-30) cc_final: 0.7572 (m-30) REVERT: I 217 ASP cc_start: 0.8650 (t0) cc_final: 0.8284 (t0) REVERT: I 228 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8587 (mmmm) REVERT: I 376 GLU cc_start: 0.8422 (tp30) cc_final: 0.7962 (tp30) REVERT: I 379 ARG cc_start: 0.9118 (tmm-80) cc_final: 0.8632 (tmm-80) REVERT: I 458 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8274 (ttp80) REVERT: I 468 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8407 (mt-10) REVERT: I 485 GLU cc_start: 0.8447 (tp30) cc_final: 0.8190 (tp30) REVERT: I 487 MET cc_start: 0.9497 (mmm) cc_final: 0.9241 (mtp) REVERT: I 492 ARG cc_start: 0.7973 (ptp-110) cc_final: 0.7757 (ptm160) REVERT: J 20 GLN cc_start: 0.9069 (mt0) cc_final: 0.8660 (mt0) REVERT: J 40 ASP cc_start: 0.8953 (t0) cc_final: 0.8458 (t0) REVERT: J 206 ASP cc_start: 0.8328 (t0) cc_final: 0.8120 (t0) REVERT: J 217 ASP cc_start: 0.8748 (t0) cc_final: 0.8385 (t0) REVERT: J 228 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8667 (mmmm) REVERT: J 346 SER cc_start: 0.9042 (m) cc_final: 0.8501 (p) REVERT: J 458 ARG cc_start: 0.8488 (ttp80) cc_final: 0.8200 (mtp-110) REVERT: J 461 GLU cc_start: 0.8111 (pm20) cc_final: 0.7750 (pm20) REVERT: J 468 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8390 (mt-10) REVERT: J 485 GLU cc_start: 0.8603 (tp30) cc_final: 0.8271 (tp30) REVERT: J 489 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7725 (tp40) REVERT: J 492 ARG cc_start: 0.8229 (ptp-170) cc_final: 0.7729 (ptp-170) REVERT: J 504 ASN cc_start: 0.8267 (m-40) cc_final: 0.7961 (m-40) REVERT: K 40 ASP cc_start: 0.8871 (t0) cc_final: 0.8245 (t0) REVERT: K 43 ASP cc_start: 0.9100 (m-30) cc_final: 0.8537 (m-30) REVERT: K 51 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: K 217 ASP cc_start: 0.8656 (t0) cc_final: 0.8292 (t0) REVERT: K 228 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8541 (mmmm) REVERT: K 346 SER cc_start: 0.9147 (m) cc_final: 0.8541 (p) REVERT: K 376 GLU cc_start: 0.8392 (tp30) cc_final: 0.8170 (tp30) REVERT: K 377 ARG cc_start: 0.9308 (ptm-80) cc_final: 0.8878 (ptm-80) REVERT: K 379 ARG cc_start: 0.9110 (tmm-80) cc_final: 0.8700 (tmm-80) REVERT: K 426 GLU cc_start: 0.8088 (tt0) cc_final: 0.7851 (tt0) REVERT: K 452 MET cc_start: 0.8966 (mmp) cc_final: 0.8462 (mmp) REVERT: K 458 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8349 (mtp-110) REVERT: K 468 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8541 (mt-10) REVERT: L 20 GLN cc_start: 0.9163 (mt0) cc_final: 0.8843 (mt0) REVERT: L 40 ASP cc_start: 0.8904 (t0) cc_final: 0.8434 (t0) REVERT: L 217 ASP cc_start: 0.8672 (t0) cc_final: 0.8310 (t0) REVERT: L 228 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8584 (mmmm) REVERT: L 376 GLU cc_start: 0.8394 (tp30) cc_final: 0.7954 (tp30) REVERT: L 379 ARG cc_start: 0.9112 (tmm-80) cc_final: 0.8627 (tmm-80) REVERT: L 452 MET cc_start: 0.8989 (mmp) cc_final: 0.8506 (mmp) REVERT: L 458 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8064 (mtp-110) REVERT: L 461 GLU cc_start: 0.8444 (pm20) cc_final: 0.7682 (pm20) REVERT: L 462 GLN cc_start: 0.8727 (tt0) cc_final: 0.8519 (tt0) REVERT: L 468 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8425 (mt-10) REVERT: L 485 GLU cc_start: 0.8476 (tp30) cc_final: 0.8174 (tp30) REVERT: L 492 ARG cc_start: 0.7969 (ptp-110) cc_final: 0.7762 (ptm160) REVERT: L 522 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8408 (ptmm) REVERT: L 523 LYS cc_start: 0.9278 (ptpp) cc_final: 0.9069 (ptpp) outliers start: 244 outliers final: 183 residues processed: 1513 average time/residue: 0.6190 time to fit residues: 1520.5283 Evaluate side-chains 1502 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1313 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 LYS Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 489 GLN Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 515 ASP Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 227 SER Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 515 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 229 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 508 ASP Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain K residue 518 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 227 SER Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 308 ILE Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 330 optimal weight: 1.9990 chunk 423 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 488 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 578 optimal weight: 0.8980 chunk 361 optimal weight: 6.9990 chunk 352 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN C 489 GLN D 76 GLN F 300 ASN G 80 GLN ** G 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 489 GLN I 80 GLN I 300 ASN K 507 ASN L 300 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 49392 Z= 0.182 Angle : 0.547 8.656 66708 Z= 0.294 Chirality : 0.042 0.246 7416 Planarity : 0.003 0.095 8496 Dihedral : 6.435 59.853 6647 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.81 % Rotamer: Outliers : 4.24 % Allowed : 17.68 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.11), residues: 5928 helix: 2.33 (0.09), residues: 2904 sheet: -0.77 (0.16), residues: 984 loop : 0.14 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 307 HIS 0.001 0.000 HIS A 296 PHE 0.021 0.001 PHE L 358 TYR 0.011 0.001 TYR L 381 ARG 0.015 0.000 ARG C 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1378 time to evaluate : 5.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9088 (mt0) cc_final: 0.8639 (mt0) REVERT: A 40 ASP cc_start: 0.8927 (t0) cc_final: 0.8495 (t0) REVERT: A 66 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8343 (mt-10) REVERT: A 217 ASP cc_start: 0.8738 (t0) cc_final: 0.8384 (t0) REVERT: A 228 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8634 (mmmm) REVERT: A 504 ASN cc_start: 0.8075 (m-40) cc_final: 0.7850 (m-40) REVERT: B 40 ASP cc_start: 0.8866 (t0) cc_final: 0.8191 (t0) REVERT: B 43 ASP cc_start: 0.9093 (m-30) cc_final: 0.8454 (m-30) REVERT: B 217 ASP cc_start: 0.8665 (t0) cc_final: 0.8255 (t0) REVERT: B 228 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8532 (mmmm) REVERT: B 376 GLU cc_start: 0.8384 (tp30) cc_final: 0.7964 (tp30) REVERT: B 377 ARG cc_start: 0.9231 (ptm-80) cc_final: 0.8909 (ptm-80) REVERT: B 426 GLU cc_start: 0.8086 (tt0) cc_final: 0.7851 (tt0) REVERT: B 452 MET cc_start: 0.8942 (mmp) cc_final: 0.8491 (mmp) REVERT: B 458 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8381 (ttp80) REVERT: B 468 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8615 (mt-10) REVERT: C 20 GLN cc_start: 0.9177 (mt0) cc_final: 0.8841 (mt0) REVERT: C 40 ASP cc_start: 0.8896 (t0) cc_final: 0.8217 (t0) REVERT: C 43 ASP cc_start: 0.9067 (m-30) cc_final: 0.8449 (m-30) REVERT: C 51 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: C 206 ASP cc_start: 0.8383 (t0) cc_final: 0.8073 (t0) REVERT: C 207 ASP cc_start: 0.8242 (m-30) cc_final: 0.7536 (m-30) REVERT: C 217 ASP cc_start: 0.8678 (t0) cc_final: 0.8302 (t0) REVERT: C 228 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8579 (mmmm) REVERT: C 376 GLU cc_start: 0.8364 (tp30) cc_final: 0.7927 (tp30) REVERT: C 379 ARG cc_start: 0.9094 (tmm-80) cc_final: 0.8590 (tmm-80) REVERT: C 452 MET cc_start: 0.8991 (mmp) cc_final: 0.8647 (mmp) REVERT: C 458 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8208 (ttp80) REVERT: D 20 GLN cc_start: 0.9095 (mt0) cc_final: 0.8595 (mt0) REVERT: D 40 ASP cc_start: 0.8944 (t0) cc_final: 0.8449 (t0) REVERT: D 217 ASP cc_start: 0.8730 (t0) cc_final: 0.8367 (t0) REVERT: D 228 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8552 (mmmm) REVERT: D 458 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8281 (mtp-110) REVERT: D 461 GLU cc_start: 0.8348 (pm20) cc_final: 0.8133 (pm20) REVERT: D 468 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8372 (mt-10) REVERT: D 485 GLU cc_start: 0.8642 (tp30) cc_final: 0.8295 (tp30) REVERT: D 504 ASN cc_start: 0.8437 (m-40) cc_final: 0.8107 (m-40) REVERT: E 40 ASP cc_start: 0.8862 (t0) cc_final: 0.8206 (t0) REVERT: E 43 ASP cc_start: 0.9083 (m-30) cc_final: 0.8504 (m-30) REVERT: E 157 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7945 (mmtt) REVERT: E 206 ASP cc_start: 0.8411 (t70) cc_final: 0.8039 (t0) REVERT: E 217 ASP cc_start: 0.8680 (t0) cc_final: 0.8247 (t0) REVERT: E 228 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8548 (mmmm) REVERT: E 346 SER cc_start: 0.9146 (m) cc_final: 0.8636 (p) REVERT: E 354 MET cc_start: 0.5018 (ptp) cc_final: 0.4675 (ptt) REVERT: E 376 GLU cc_start: 0.8391 (tp30) cc_final: 0.7986 (tp30) REVERT: E 458 ARG cc_start: 0.8544 (ttp80) cc_final: 0.8212 (ttp80) REVERT: E 468 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8580 (mt-10) REVERT: E 485 GLU cc_start: 0.8516 (tp30) cc_final: 0.8156 (tp30) REVERT: F 40 ASP cc_start: 0.8892 (t0) cc_final: 0.8412 (t0) REVERT: F 51 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: F 206 ASP cc_start: 0.8256 (t0) cc_final: 0.7845 (t0) REVERT: F 207 ASP cc_start: 0.8167 (m-30) cc_final: 0.7608 (m-30) REVERT: F 217 ASP cc_start: 0.8653 (t0) cc_final: 0.8277 (t0) REVERT: F 228 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8607 (mmmm) REVERT: F 376 GLU cc_start: 0.8381 (tp30) cc_final: 0.7941 (tp30) REVERT: F 379 ARG cc_start: 0.9099 (tmm-80) cc_final: 0.8606 (tmm-80) REVERT: F 458 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8324 (ttp80) REVERT: F 461 GLU cc_start: 0.8401 (pm20) cc_final: 0.8147 (pm20) REVERT: F 462 GLN cc_start: 0.8715 (tt0) cc_final: 0.8495 (tt0) REVERT: F 468 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8292 (mt-10) REVERT: F 485 GLU cc_start: 0.8534 (tp30) cc_final: 0.8253 (tp30) REVERT: F 522 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8830 (tmtt) REVERT: F 523 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9031 (ptpp) REVERT: G 20 GLN cc_start: 0.9072 (mt0) cc_final: 0.8538 (mt0) REVERT: G 40 ASP cc_start: 0.8955 (t0) cc_final: 0.8518 (t0) REVERT: G 135 GLU cc_start: 0.7533 (pm20) cc_final: 0.7298 (pm20) REVERT: G 217 ASP cc_start: 0.8732 (t0) cc_final: 0.8359 (t0) REVERT: G 376 GLU cc_start: 0.8399 (tp30) cc_final: 0.7322 (tp30) REVERT: G 426 GLU cc_start: 0.8143 (tt0) cc_final: 0.7864 (tt0) REVERT: G 458 ARG cc_start: 0.8580 (mtm110) cc_final: 0.8093 (mtm-85) REVERT: G 468 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8659 (mt-10) REVERT: G 485 GLU cc_start: 0.8640 (tp30) cc_final: 0.8318 (tp30) REVERT: G 492 ARG cc_start: 0.8041 (ptm160) cc_final: 0.7002 (ptm160) REVERT: G 504 ASN cc_start: 0.8374 (m-40) cc_final: 0.8037 (m-40) REVERT: H 40 ASP cc_start: 0.8852 (t0) cc_final: 0.8190 (t0) REVERT: H 43 ASP cc_start: 0.9092 (m-30) cc_final: 0.8504 (m-30) REVERT: H 217 ASP cc_start: 0.8677 (t0) cc_final: 0.8249 (t0) REVERT: H 228 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8548 (mmmm) REVERT: H 346 SER cc_start: 0.9025 (m) cc_final: 0.8471 (p) REVERT: H 354 MET cc_start: 0.5433 (ptp) cc_final: 0.5169 (ptt) REVERT: H 377 ARG cc_start: 0.9232 (ptm-80) cc_final: 0.8942 (ptm-80) REVERT: H 379 ARG cc_start: 0.9110 (tmm-80) cc_final: 0.8834 (ttp-170) REVERT: H 458 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8191 (ttp80) REVERT: H 468 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8610 (mt-10) REVERT: H 504 ASN cc_start: 0.8437 (m-40) cc_final: 0.8210 (m110) REVERT: H 523 LYS cc_start: 0.9408 (pptt) cc_final: 0.9152 (ptpp) REVERT: I 20 GLN cc_start: 0.9166 (mt0) cc_final: 0.8765 (mt0) REVERT: I 40 ASP cc_start: 0.8902 (t0) cc_final: 0.8217 (t0) REVERT: I 43 ASP cc_start: 0.9077 (m-30) cc_final: 0.8455 (m-30) REVERT: I 48 ARG cc_start: 0.6452 (tpt170) cc_final: 0.6128 (tpt170) REVERT: I 51 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: I 206 ASP cc_start: 0.8397 (t0) cc_final: 0.8094 (t0) REVERT: I 207 ASP cc_start: 0.8244 (m-30) cc_final: 0.7557 (m-30) REVERT: I 217 ASP cc_start: 0.8648 (t0) cc_final: 0.8271 (t0) REVERT: I 228 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8573 (mmmm) REVERT: I 376 GLU cc_start: 0.8376 (tp30) cc_final: 0.7932 (tp30) REVERT: I 379 ARG cc_start: 0.9102 (tmm-80) cc_final: 0.8599 (tmm-80) REVERT: I 452 MET cc_start: 0.8951 (mmp) cc_final: 0.8679 (mmp) REVERT: I 458 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8232 (ttp80) REVERT: I 461 GLU cc_start: 0.8310 (pm20) cc_final: 0.7961 (pm20) REVERT: I 468 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8412 (mt-10) REVERT: I 485 GLU cc_start: 0.8447 (tp30) cc_final: 0.8165 (tp30) REVERT: I 492 ARG cc_start: 0.7911 (ptp-110) cc_final: 0.7694 (ptm160) REVERT: I 523 LYS cc_start: 0.9362 (pptt) cc_final: 0.9113 (ptpp) REVERT: J 20 GLN cc_start: 0.9078 (mt0) cc_final: 0.8668 (mt0) REVERT: J 40 ASP cc_start: 0.8952 (t0) cc_final: 0.8476 (t0) REVERT: J 109 ARG cc_start: 0.9042 (tpp80) cc_final: 0.8792 (tpp80) REVERT: J 110 ASN cc_start: 0.8799 (m-40) cc_final: 0.8050 (m-40) REVERT: J 206 ASP cc_start: 0.8324 (t0) cc_final: 0.8106 (t0) REVERT: J 217 ASP cc_start: 0.8744 (t0) cc_final: 0.8381 (t0) REVERT: J 228 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8660 (mmmm) REVERT: J 346 SER cc_start: 0.9039 (m) cc_final: 0.8510 (p) REVERT: J 426 GLU cc_start: 0.8086 (tt0) cc_final: 0.7844 (tt0) REVERT: J 458 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8209 (mtp-110) REVERT: J 461 GLU cc_start: 0.8151 (pm20) cc_final: 0.7650 (pm20) REVERT: J 468 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8440 (mt-10) REVERT: J 485 GLU cc_start: 0.8585 (tp30) cc_final: 0.8223 (tp30) REVERT: J 489 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7651 (tp40) REVERT: J 492 ARG cc_start: 0.8248 (ptp-170) cc_final: 0.7634 (ptp-170) REVERT: J 504 ASN cc_start: 0.8252 (m-40) cc_final: 0.7942 (m-40) REVERT: K 40 ASP cc_start: 0.8863 (t0) cc_final: 0.8206 (t0) REVERT: K 43 ASP cc_start: 0.9095 (m-30) cc_final: 0.8510 (m-30) REVERT: K 217 ASP cc_start: 0.8666 (t0) cc_final: 0.8257 (t0) REVERT: K 228 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8526 (mmmm) REVERT: K 346 SER cc_start: 0.9187 (m) cc_final: 0.8672 (p) REVERT: K 376 GLU cc_start: 0.8392 (tp30) cc_final: 0.8009 (tp30) REVERT: K 377 ARG cc_start: 0.9303 (ptm-80) cc_final: 0.8915 (ptm-80) REVERT: K 452 MET cc_start: 0.8973 (mmp) cc_final: 0.8525 (mmp) REVERT: K 458 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8243 (mtp-110) REVERT: K 461 GLU cc_start: 0.8316 (pm20) cc_final: 0.7888 (pm20) REVERT: K 468 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8594 (mt-10) REVERT: K 504 ASN cc_start: 0.8646 (m-40) cc_final: 0.7703 (m110) REVERT: L 20 GLN cc_start: 0.9176 (mt0) cc_final: 0.8855 (mt0) REVERT: L 40 ASP cc_start: 0.8901 (t0) cc_final: 0.8223 (t0) REVERT: L 43 ASP cc_start: 0.9079 (m-30) cc_final: 0.8463 (m-30) REVERT: L 51 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: L 217 ASP cc_start: 0.8674 (t0) cc_final: 0.8302 (t0) REVERT: L 228 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8577 (mmmm) REVERT: L 376 GLU cc_start: 0.8376 (tp30) cc_final: 0.7927 (tp30) REVERT: L 379 ARG cc_start: 0.9104 (tmm-80) cc_final: 0.8611 (tmm-80) REVERT: L 452 MET cc_start: 0.8980 (mmp) cc_final: 0.8559 (mmp) REVERT: L 458 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8215 (ttp80) REVERT: L 461 GLU cc_start: 0.8432 (pm20) cc_final: 0.8215 (pm20) REVERT: L 462 GLN cc_start: 0.8727 (tt0) cc_final: 0.8495 (tt0) REVERT: L 468 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8395 (mt-10) REVERT: L 485 GLU cc_start: 0.8456 (tp30) cc_final: 0.8136 (tp30) REVERT: L 492 ARG cc_start: 0.7833 (ptp-110) cc_final: 0.7594 (ptm160) REVERT: L 522 LYS cc_start: 0.8992 (ttpp) cc_final: 0.8417 (ptmm) outliers start: 227 outliers final: 186 residues processed: 1476 average time/residue: 0.6311 time to fit residues: 1519.9333 Evaluate side-chains 1507 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1314 time to evaluate : 5.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 LYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 489 GLN Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 515 ASP Chi-restraints excluded: chain H residue 518 LEU Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 515 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 229 ILE Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 458 ARG Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain K residue 518 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 308 ILE Chi-restraints excluded: chain L residue 377 ARG Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 10.0000 chunk 230 optimal weight: 0.6980 chunk 345 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 367 optimal weight: 8.9990 chunk 393 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 454 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 507 ASN F 80 GLN G 296 HIS G 526 ASN H 489 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 49392 Z= 0.246 Angle : 0.575 8.817 66708 Z= 0.310 Chirality : 0.043 0.244 7416 Planarity : 0.003 0.052 8496 Dihedral : 6.407 59.918 6645 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 4.28 % Allowed : 18.22 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.11), residues: 5928 helix: 2.22 (0.09), residues: 2952 sheet: -0.76 (0.16), residues: 984 loop : -0.04 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 307 HIS 0.002 0.001 HIS K 433 PHE 0.016 0.001 PHE F 358 TYR 0.014 0.001 TYR H 3 ARG 0.009 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1562 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 1333 time to evaluate : 5.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9137 (mt0) cc_final: 0.8726 (mt0) REVERT: A 40 ASP cc_start: 0.8930 (t0) cc_final: 0.8431 (t0) REVERT: A 66 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 217 ASP cc_start: 0.8737 (t0) cc_final: 0.8384 (t0) REVERT: A 228 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8604 (mmmm) REVERT: A 504 ASN cc_start: 0.8137 (m-40) cc_final: 0.7918 (m-40) REVERT: A 523 LYS cc_start: 0.9039 (ptpp) cc_final: 0.8838 (ptpp) REVERT: B 40 ASP cc_start: 0.8874 (t0) cc_final: 0.8185 (t0) REVERT: B 43 ASP cc_start: 0.9106 (m-30) cc_final: 0.8424 (m-30) REVERT: B 217 ASP cc_start: 0.8677 (t0) cc_final: 0.8251 (t0) REVERT: B 228 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8520 (mmmm) REVERT: B 376 GLU cc_start: 0.8387 (tp30) cc_final: 0.8133 (tp30) REVERT: B 377 ARG cc_start: 0.9237 (ptm-80) cc_final: 0.8910 (ptm-80) REVERT: B 426 GLU cc_start: 0.8083 (tt0) cc_final: 0.7880 (tt0) REVERT: B 452 MET cc_start: 0.8992 (mmp) cc_final: 0.8540 (mmp) REVERT: B 458 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8335 (ttp80) REVERT: B 468 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8578 (mt-10) REVERT: C 20 GLN cc_start: 0.9183 (mt0) cc_final: 0.8844 (mt0) REVERT: C 40 ASP cc_start: 0.8898 (t0) cc_final: 0.8220 (t0) REVERT: C 43 ASP cc_start: 0.9085 (m-30) cc_final: 0.8456 (m-30) REVERT: C 51 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: C 206 ASP cc_start: 0.8426 (t0) cc_final: 0.8087 (t0) REVERT: C 207 ASP cc_start: 0.8274 (m-30) cc_final: 0.7565 (m-30) REVERT: C 217 ASP cc_start: 0.8628 (t0) cc_final: 0.8312 (t0) REVERT: C 228 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8578 (mmmm) REVERT: C 376 GLU cc_start: 0.8396 (tp30) cc_final: 0.8108 (tp30) REVERT: D 20 GLN cc_start: 0.9134 (mt0) cc_final: 0.8665 (mt0) REVERT: D 40 ASP cc_start: 0.8943 (t0) cc_final: 0.8477 (t0) REVERT: D 217 ASP cc_start: 0.8728 (t0) cc_final: 0.8367 (t0) REVERT: D 228 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8593 (mmmm) REVERT: D 458 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8294 (mtp-110) REVERT: D 468 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8422 (mt-10) REVERT: D 485 GLU cc_start: 0.8646 (tp30) cc_final: 0.8272 (tp30) REVERT: D 504 ASN cc_start: 0.8451 (m-40) cc_final: 0.8134 (m-40) REVERT: E 40 ASP cc_start: 0.8870 (t0) cc_final: 0.8212 (t0) REVERT: E 43 ASP cc_start: 0.9095 (m-30) cc_final: 0.8511 (m-30) REVERT: E 206 ASP cc_start: 0.8429 (t70) cc_final: 0.8065 (t0) REVERT: E 217 ASP cc_start: 0.8672 (t0) cc_final: 0.8241 (t0) REVERT: E 228 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8527 (mmmm) REVERT: E 346 SER cc_start: 0.9149 (m) cc_final: 0.8716 (p) REVERT: E 354 MET cc_start: 0.5377 (ptp) cc_final: 0.5125 (ptt) REVERT: E 376 GLU cc_start: 0.8401 (tp30) cc_final: 0.8019 (tp30) REVERT: E 377 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8908 (ptm-80) REVERT: E 458 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8100 (mtp-110) REVERT: E 461 GLU cc_start: 0.8161 (pm20) cc_final: 0.7879 (pm20) REVERT: E 468 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8542 (mt-10) REVERT: E 485 GLU cc_start: 0.8538 (tp30) cc_final: 0.8172 (tp30) REVERT: F 20 GLN cc_start: 0.9180 (mt0) cc_final: 0.8838 (mt0) REVERT: F 40 ASP cc_start: 0.8902 (t0) cc_final: 0.8424 (t0) REVERT: F 206 ASP cc_start: 0.8319 (t0) cc_final: 0.7865 (t0) REVERT: F 207 ASP cc_start: 0.8213 (m-30) cc_final: 0.7615 (m-30) REVERT: F 217 ASP cc_start: 0.8614 (t0) cc_final: 0.8301 (t0) REVERT: F 228 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8625 (mmmm) REVERT: F 346 SER cc_start: 0.9198 (m) cc_final: 0.8606 (p) REVERT: F 376 GLU cc_start: 0.8408 (tp30) cc_final: 0.7936 (tp30) REVERT: F 379 ARG cc_start: 0.9104 (tmm-80) cc_final: 0.8574 (tmm-80) REVERT: F 462 GLN cc_start: 0.8741 (tt0) cc_final: 0.8508 (tt0) REVERT: F 468 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8364 (mt-10) REVERT: F 485 GLU cc_start: 0.8550 (tp30) cc_final: 0.8258 (tp30) REVERT: F 522 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8845 (tmtt) REVERT: F 523 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9029 (ptpp) REVERT: G 20 GLN cc_start: 0.9121 (mt0) cc_final: 0.8621 (mt0) REVERT: G 40 ASP cc_start: 0.8943 (t0) cc_final: 0.8493 (t0) REVERT: G 135 GLU cc_start: 0.7533 (pm20) cc_final: 0.7295 (pm20) REVERT: G 217 ASP cc_start: 0.8714 (t0) cc_final: 0.8408 (t0) REVERT: G 426 GLU cc_start: 0.8155 (tt0) cc_final: 0.7876 (tt0) REVERT: G 458 ARG cc_start: 0.8590 (mtm110) cc_final: 0.8050 (mtm-85) REVERT: G 468 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8643 (mt-10) REVERT: G 485 GLU cc_start: 0.8651 (tp30) cc_final: 0.8337 (tp30) REVERT: G 504 ASN cc_start: 0.8369 (m-40) cc_final: 0.8036 (m-40) REVERT: H 40 ASP cc_start: 0.8861 (t0) cc_final: 0.8133 (t0) REVERT: H 43 ASP cc_start: 0.9112 (m-30) cc_final: 0.8483 (m-30) REVERT: H 217 ASP cc_start: 0.8666 (t0) cc_final: 0.8235 (t0) REVERT: H 228 LYS cc_start: 0.8911 (mmmm) cc_final: 0.8556 (mmmm) REVERT: H 346 SER cc_start: 0.9045 (m) cc_final: 0.8535 (p) REVERT: H 354 MET cc_start: 0.5376 (ptp) cc_final: 0.4148 (tpp) REVERT: H 458 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8293 (ttp80) REVERT: H 468 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8617 (mt-10) REVERT: H 504 ASN cc_start: 0.8464 (m-40) cc_final: 0.8253 (m110) REVERT: I 20 GLN cc_start: 0.9181 (mt0) cc_final: 0.8785 (mt0) REVERT: I 40 ASP cc_start: 0.8913 (t0) cc_final: 0.8225 (t0) REVERT: I 43 ASP cc_start: 0.9084 (m-30) cc_final: 0.8438 (m-30) REVERT: I 48 ARG cc_start: 0.6425 (tpt170) cc_final: 0.6130 (tpt170) REVERT: I 51 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: I 217 ASP cc_start: 0.8626 (t0) cc_final: 0.8314 (t0) REVERT: I 228 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8585 (mmmm) REVERT: I 376 GLU cc_start: 0.8405 (tp30) cc_final: 0.7920 (tp30) REVERT: I 379 ARG cc_start: 0.9105 (tmm-80) cc_final: 0.8577 (tmm-80) REVERT: I 458 ARG cc_start: 0.8561 (ttp80) cc_final: 0.8205 (ttp80) REVERT: I 461 GLU cc_start: 0.8279 (pm20) cc_final: 0.7841 (pm20) REVERT: I 468 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8414 (mt-10) REVERT: I 485 GLU cc_start: 0.8469 (tp30) cc_final: 0.8208 (tp30) REVERT: I 487 MET cc_start: 0.9487 (mmm) cc_final: 0.9286 (mtp) REVERT: I 513 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8184 (t0) REVERT: J 20 GLN cc_start: 0.9130 (mt0) cc_final: 0.8794 (mt0) REVERT: J 40 ASP cc_start: 0.8958 (t0) cc_final: 0.8492 (t0) REVERT: J 109 ARG cc_start: 0.8997 (tpp80) cc_final: 0.8765 (tpp80) REVERT: J 110 ASN cc_start: 0.8768 (m-40) cc_final: 0.7900 (m-40) REVERT: J 217 ASP cc_start: 0.8717 (t0) cc_final: 0.8364 (t0) REVERT: J 228 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8670 (mmmm) REVERT: J 346 SER cc_start: 0.9116 (m) cc_final: 0.8575 (p) REVERT: J 426 GLU cc_start: 0.8048 (tt0) cc_final: 0.7786 (tt0) REVERT: J 458 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8237 (mtp-110) REVERT: J 461 GLU cc_start: 0.8150 (pm20) cc_final: 0.7585 (pm20) REVERT: J 468 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8452 (mt-10) REVERT: J 485 GLU cc_start: 0.8619 (tp30) cc_final: 0.8255 (tp30) REVERT: J 489 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7649 (tp40) REVERT: J 492 ARG cc_start: 0.8317 (ptp-170) cc_final: 0.7663 (ptp-170) REVERT: J 504 ASN cc_start: 0.8317 (m-40) cc_final: 0.8021 (m-40) REVERT: J 523 LYS cc_start: 0.9120 (ptpp) cc_final: 0.8891 (ptpp) REVERT: K 40 ASP cc_start: 0.8874 (t0) cc_final: 0.8188 (t0) REVERT: K 43 ASP cc_start: 0.9107 (m-30) cc_final: 0.8419 (m-30) REVERT: K 217 ASP cc_start: 0.8680 (t0) cc_final: 0.8253 (t0) REVERT: K 228 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8516 (mmmm) REVERT: K 346 SER cc_start: 0.9180 (m) cc_final: 0.8732 (p) REVERT: K 376 GLU cc_start: 0.8399 (tp30) cc_final: 0.8118 (tp30) REVERT: K 452 MET cc_start: 0.9026 (mmp) cc_final: 0.8578 (mmp) REVERT: K 458 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8269 (mtp-110) REVERT: K 461 GLU cc_start: 0.8334 (pm20) cc_final: 0.8124 (pm20) REVERT: K 468 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8551 (mt-10) REVERT: L 1 MET cc_start: 0.8112 (ppp) cc_final: 0.7640 (ppp) REVERT: L 20 GLN cc_start: 0.9181 (mt0) cc_final: 0.8842 (mt0) REVERT: L 40 ASP cc_start: 0.8911 (t0) cc_final: 0.8229 (t0) REVERT: L 43 ASP cc_start: 0.9091 (m-30) cc_final: 0.8467 (m-30) REVERT: L 51 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: L 217 ASP cc_start: 0.8627 (t0) cc_final: 0.8313 (t0) REVERT: L 228 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8586 (mmmm) REVERT: L 376 GLU cc_start: 0.8414 (tp30) cc_final: 0.8116 (tp30) REVERT: L 458 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8030 (ttp80) REVERT: L 461 GLU cc_start: 0.8385 (pm20) cc_final: 0.8130 (pm20) REVERT: L 462 GLN cc_start: 0.8715 (tt0) cc_final: 0.8510 (tt0) REVERT: L 468 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8388 (mt-10) REVERT: L 485 GLU cc_start: 0.8486 (tp30) cc_final: 0.8168 (tp30) outliers start: 229 outliers final: 198 residues processed: 1433 average time/residue: 0.6304 time to fit residues: 1471.7947 Evaluate side-chains 1499 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1293 time to evaluate : 5.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 LYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 270 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 489 GLN Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 515 ASP Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 377 ARG Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 457 VAL Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 515 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 458 ARG Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain K residue 518 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 270 MET Chi-restraints excluded: chain L residue 308 ILE Chi-restraints excluded: chain L residue 377 ARG Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 5.9990 chunk 554 optimal weight: 2.9990 chunk 505 optimal weight: 6.9990 chunk 538 optimal weight: 5.9990 chunk 553 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 423 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 486 optimal weight: 10.0000 chunk 509 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 507 ASN C 300 ASN G 489 GLN H 489 GLN K 504 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 49392 Z= 0.298 Angle : 0.606 9.701 66708 Z= 0.326 Chirality : 0.043 0.242 7416 Planarity : 0.003 0.074 8496 Dihedral : 6.374 59.758 6638 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.12 % Favored : 96.68 % Rotamer: Outliers : 4.35 % Allowed : 18.37 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.11), residues: 5928 helix: 2.18 (0.09), residues: 2952 sheet: -0.80 (0.16), residues: 984 loop : -0.09 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 307 HIS 0.002 0.001 HIS K 433 PHE 0.020 0.002 PHE H 161 TYR 0.012 0.001 TYR J 381 ARG 0.016 0.001 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1542 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 1309 time to evaluate : 5.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9158 (mt0) cc_final: 0.8731 (mt0) REVERT: A 40 ASP cc_start: 0.8934 (t0) cc_final: 0.8494 (t0) REVERT: A 48 ARG cc_start: 0.6408 (tpt170) cc_final: 0.6203 (tpt170) REVERT: A 66 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8345 (mt-10) REVERT: A 217 ASP cc_start: 0.8729 (t0) cc_final: 0.8375 (t0) REVERT: A 228 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8615 (mmmm) REVERT: A 492 ARG cc_start: 0.8126 (ptp-110) cc_final: 0.7800 (ptp90) REVERT: A 504 ASN cc_start: 0.8106 (m-40) cc_final: 0.7875 (m-40) REVERT: B 40 ASP cc_start: 0.8880 (t0) cc_final: 0.8218 (t0) REVERT: B 43 ASP cc_start: 0.9116 (m-30) cc_final: 0.8495 (m-30) REVERT: B 217 ASP cc_start: 0.8674 (t0) cc_final: 0.8244 (t0) REVERT: B 228 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8542 (mmmm) REVERT: B 290 LEU cc_start: 0.9749 (mt) cc_final: 0.9515 (mt) REVERT: B 376 GLU cc_start: 0.8379 (tp30) cc_final: 0.8087 (tp30) REVERT: B 377 ARG cc_start: 0.9247 (ptm-80) cc_final: 0.8909 (ptm-80) REVERT: B 452 MET cc_start: 0.9025 (mmp) cc_final: 0.8572 (mmp) REVERT: B 458 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8390 (ttp80) REVERT: B 468 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8563 (mt-10) REVERT: C 20 GLN cc_start: 0.9195 (mt0) cc_final: 0.8856 (mt0) REVERT: C 40 ASP cc_start: 0.8913 (t0) cc_final: 0.8443 (t0) REVERT: C 51 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: C 217 ASP cc_start: 0.8627 (t0) cc_final: 0.8243 (t0) REVERT: C 228 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8589 (mmmm) REVERT: C 376 GLU cc_start: 0.8421 (tp30) cc_final: 0.8128 (tp30) REVERT: C 458 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8401 (ttp80) REVERT: D 20 GLN cc_start: 0.9136 (mt0) cc_final: 0.8704 (mt0) REVERT: D 40 ASP cc_start: 0.8951 (t0) cc_final: 0.8518 (t0) REVERT: D 217 ASP cc_start: 0.8717 (t0) cc_final: 0.8350 (t0) REVERT: D 228 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8588 (mmmm) REVERT: D 376 GLU cc_start: 0.8186 (tp30) cc_final: 0.7427 (tp30) REVERT: D 379 ARG cc_start: 0.9079 (tmm-80) cc_final: 0.8770 (tmm-80) REVERT: D 458 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (mtp-110) REVERT: D 461 GLU cc_start: 0.8366 (pm20) cc_final: 0.8090 (pm20) REVERT: D 468 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8432 (mt-10) REVERT: D 485 GLU cc_start: 0.8680 (tp30) cc_final: 0.8434 (tp30) REVERT: D 504 ASN cc_start: 0.8420 (m-40) cc_final: 0.8106 (m-40) REVERT: E 40 ASP cc_start: 0.8886 (t0) cc_final: 0.8233 (t0) REVERT: E 43 ASP cc_start: 0.9115 (m-30) cc_final: 0.8553 (m-30) REVERT: E 206 ASP cc_start: 0.8503 (t70) cc_final: 0.8189 (t0) REVERT: E 217 ASP cc_start: 0.8663 (t0) cc_final: 0.8229 (t0) REVERT: E 228 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8540 (mmmm) REVERT: E 346 SER cc_start: 0.9138 (m) cc_final: 0.8733 (p) REVERT: E 354 MET cc_start: 0.5417 (ptp) cc_final: 0.4123 (tpp) REVERT: E 376 GLU cc_start: 0.8402 (tp30) cc_final: 0.8093 (tp30) REVERT: E 377 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8913 (ptm-80) REVERT: E 458 ARG cc_start: 0.8561 (ttp80) cc_final: 0.8068 (mtp-110) REVERT: E 461 GLU cc_start: 0.8199 (pm20) cc_final: 0.7875 (pm20) REVERT: E 468 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8536 (mt-10) REVERT: E 485 GLU cc_start: 0.8554 (tp30) cc_final: 0.8166 (tp30) REVERT: E 492 ARG cc_start: 0.7986 (ptp-170) cc_final: 0.7122 (ptp-170) REVERT: E 523 LYS cc_start: 0.9067 (ptpp) cc_final: 0.8861 (ptpp) REVERT: F 20 GLN cc_start: 0.9193 (mt0) cc_final: 0.8855 (mt0) REVERT: F 40 ASP cc_start: 0.8915 (t0) cc_final: 0.8450 (t0) REVERT: F 51 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: F 217 ASP cc_start: 0.8610 (t0) cc_final: 0.8290 (t0) REVERT: F 228 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8631 (mmmm) REVERT: F 346 SER cc_start: 0.9204 (m) cc_final: 0.8595 (p) REVERT: F 376 GLU cc_start: 0.8418 (tp30) cc_final: 0.8117 (tp30) REVERT: F 468 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8402 (mt-10) REVERT: F 522 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8858 (tmtt) REVERT: F 523 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9045 (ptpp) REVERT: G 20 GLN cc_start: 0.9148 (mt0) cc_final: 0.8694 (mt0) REVERT: G 40 ASP cc_start: 0.8945 (t0) cc_final: 0.8502 (t0) REVERT: G 66 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8652 (mt-10) REVERT: G 217 ASP cc_start: 0.8706 (t0) cc_final: 0.8405 (t0) REVERT: G 458 ARG cc_start: 0.8568 (mtm110) cc_final: 0.8361 (mtm110) REVERT: G 468 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8639 (mt-10) REVERT: G 485 GLU cc_start: 0.8673 (tp30) cc_final: 0.8379 (tp30) REVERT: G 504 ASN cc_start: 0.8353 (m-40) cc_final: 0.8024 (m-40) REVERT: H 40 ASP cc_start: 0.8880 (t0) cc_final: 0.8177 (t0) REVERT: H 43 ASP cc_start: 0.9121 (m-30) cc_final: 0.8649 (m-30) REVERT: H 217 ASP cc_start: 0.8662 (t0) cc_final: 0.8226 (t0) REVERT: H 228 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8530 (mmmm) REVERT: H 308 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9282 (pp) REVERT: H 346 SER cc_start: 0.9026 (m) cc_final: 0.8539 (p) REVERT: H 354 MET cc_start: 0.5407 (ptp) cc_final: 0.4120 (tpp) REVERT: H 455 TYR cc_start: 0.7880 (m-80) cc_final: 0.7208 (m-80) REVERT: H 458 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8354 (ttp80) REVERT: H 468 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8556 (mt-10) REVERT: H 489 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8931 (tp40) REVERT: I 20 GLN cc_start: 0.9194 (mt0) cc_final: 0.8862 (mt0) REVERT: I 40 ASP cc_start: 0.8928 (t0) cc_final: 0.8252 (t0) REVERT: I 43 ASP cc_start: 0.9118 (m-30) cc_final: 0.8494 (m-30) REVERT: I 48 ARG cc_start: 0.6466 (tpt170) cc_final: 0.6124 (tpt170) REVERT: I 51 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: I 217 ASP cc_start: 0.8606 (t0) cc_final: 0.8289 (t0) REVERT: I 228 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8595 (mmmm) REVERT: I 376 GLU cc_start: 0.8433 (tp30) cc_final: 0.8139 (tp30) REVERT: I 458 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8185 (ttp80) REVERT: I 461 GLU cc_start: 0.8274 (pm20) cc_final: 0.7797 (pm20) REVERT: I 468 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8420 (mt-10) REVERT: I 487 MET cc_start: 0.9495 (mmm) cc_final: 0.9282 (mtp) REVERT: I 513 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8233 (t0) REVERT: J 20 GLN cc_start: 0.9157 (mt0) cc_final: 0.8779 (mt0) REVERT: J 40 ASP cc_start: 0.8963 (t0) cc_final: 0.8535 (t0) REVERT: J 109 ARG cc_start: 0.9005 (tpp80) cc_final: 0.8775 (tpp80) REVERT: J 110 ASN cc_start: 0.8772 (m-40) cc_final: 0.8544 (m-40) REVERT: J 217 ASP cc_start: 0.8711 (t0) cc_final: 0.8346 (t0) REVERT: J 228 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8634 (mmmm) REVERT: J 346 SER cc_start: 0.9111 (m) cc_final: 0.8608 (p) REVERT: J 379 ARG cc_start: 0.9221 (tmm-80) cc_final: 0.9004 (tmm-80) REVERT: J 468 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8464 (mt-10) REVERT: J 485 GLU cc_start: 0.8658 (tp30) cc_final: 0.8409 (tp30) REVERT: J 489 GLN cc_start: 0.8198 (tp-100) cc_final: 0.7681 (tp40) REVERT: J 492 ARG cc_start: 0.8336 (ptp-170) cc_final: 0.7703 (ptp-170) REVERT: J 504 ASN cc_start: 0.8308 (m-40) cc_final: 0.8037 (m-40) REVERT: K 40 ASP cc_start: 0.8879 (t0) cc_final: 0.8220 (t0) REVERT: K 43 ASP cc_start: 0.9116 (m-30) cc_final: 0.8491 (m-30) REVERT: K 217 ASP cc_start: 0.8675 (t0) cc_final: 0.8240 (t0) REVERT: K 228 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8538 (mmmm) REVERT: K 346 SER cc_start: 0.9171 (m) cc_final: 0.8759 (p) REVERT: K 376 GLU cc_start: 0.8385 (tp30) cc_final: 0.8087 (tp30) REVERT: K 377 ARG cc_start: 0.9312 (ptm-80) cc_final: 0.8927 (ptm-80) REVERT: K 452 MET cc_start: 0.9072 (mmp) cc_final: 0.8561 (mmp) REVERT: K 455 TYR cc_start: 0.7846 (m-80) cc_final: 0.6639 (m-80) REVERT: K 458 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8219 (mtp-110) REVERT: K 461 GLU cc_start: 0.8334 (pm20) cc_final: 0.7874 (pm20) REVERT: K 468 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8537 (mt-10) REVERT: L 1 MET cc_start: 0.8178 (ppp) cc_final: 0.7734 (ppp) REVERT: L 20 GLN cc_start: 0.9194 (mt0) cc_final: 0.8856 (mt0) REVERT: L 40 ASP cc_start: 0.8925 (t0) cc_final: 0.8254 (t0) REVERT: L 43 ASP cc_start: 0.9115 (m-30) cc_final: 0.8478 (m-30) REVERT: L 51 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: L 217 ASP cc_start: 0.8626 (t0) cc_final: 0.8307 (t0) REVERT: L 228 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8586 (mmmm) REVERT: L 376 GLU cc_start: 0.8416 (tp30) cc_final: 0.8105 (tp30) REVERT: L 458 ARG cc_start: 0.8473 (ttp80) cc_final: 0.7920 (mtp-110) REVERT: L 461 GLU cc_start: 0.8383 (pm20) cc_final: 0.7492 (pm20) REVERT: L 468 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8398 (mt-10) REVERT: L 485 GLU cc_start: 0.8507 (tp30) cc_final: 0.8183 (tp30) outliers start: 233 outliers final: 209 residues processed: 1411 average time/residue: 0.6725 time to fit residues: 1552.1647 Evaluate side-chains 1509 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1289 time to evaluate : 5.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 515 ASP Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 LYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 270 MET Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 489 GLN Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 515 ASP Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 457 VAL Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 515 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 270 MET Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 458 ARG Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain K residue 518 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 270 MET Chi-restraints excluded: chain L residue 308 ILE Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 377 ARG Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 20.0000 chunk 353 optimal weight: 20.0000 chunk 569 optimal weight: 0.9990 chunk 347 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 396 optimal weight: 7.9990 chunk 597 optimal weight: 6.9990 chunk 550 optimal weight: 10.0000 chunk 475 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 367 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 GLN H 489 GLN H 504 ASN K 507 ASN L 504 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 49392 Z= 0.269 Angle : 0.620 10.451 66708 Z= 0.332 Chirality : 0.043 0.253 7416 Planarity : 0.004 0.097 8496 Dihedral : 6.356 59.629 6638 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.85 % Favored : 96.95 % Rotamer: Outliers : 4.24 % Allowed : 18.55 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.11), residues: 5928 helix: 2.14 (0.09), residues: 2952 sheet: -0.81 (0.16), residues: 984 loop : -0.09 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 307 HIS 0.002 0.001 HIS E 433 PHE 0.023 0.001 PHE H 161 TYR 0.011 0.001 TYR L 381 ARG 0.014 0.001 ARG B 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11856 Ramachandran restraints generated. 5928 Oldfield, 0 Emsley, 5928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1319 time to evaluate : 5.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.9153 (mt0) cc_final: 0.8725 (mt0) REVERT: A 40 ASP cc_start: 0.8924 (t0) cc_final: 0.8466 (t0) REVERT: A 48 ARG cc_start: 0.6363 (tpt170) cc_final: 0.6142 (tpt170) REVERT: A 66 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 217 ASP cc_start: 0.8729 (t0) cc_final: 0.8373 (t0) REVERT: A 228 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8619 (mmmm) REVERT: A 354 MET cc_start: 0.5690 (ptp) cc_final: 0.4063 (tpp) REVERT: A 458 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8271 (ttp80) REVERT: A 461 GLU cc_start: 0.8495 (pm20) cc_final: 0.8240 (pm20) REVERT: A 504 ASN cc_start: 0.8107 (m-40) cc_final: 0.7884 (m-40) REVERT: A 523 LYS cc_start: 0.9028 (ptpp) cc_final: 0.8769 (ptpp) REVERT: B 40 ASP cc_start: 0.8876 (t0) cc_final: 0.8137 (t0) REVERT: B 43 ASP cc_start: 0.9114 (m-30) cc_final: 0.8482 (m-30) REVERT: B 217 ASP cc_start: 0.8664 (t0) cc_final: 0.8231 (t0) REVERT: B 228 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8537 (mmmm) REVERT: B 376 GLU cc_start: 0.8394 (tp30) cc_final: 0.8030 (tp30) REVERT: B 377 ARG cc_start: 0.9237 (ptm-80) cc_final: 0.8894 (ptm-80) REVERT: B 452 MET cc_start: 0.8981 (mmp) cc_final: 0.8567 (mmp) REVERT: B 458 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8321 (ttp80) REVERT: B 468 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8549 (mt-10) REVERT: C 20 GLN cc_start: 0.9189 (mt0) cc_final: 0.8852 (mt0) REVERT: C 40 ASP cc_start: 0.8911 (t0) cc_final: 0.8448 (t0) REVERT: C 51 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: C 217 ASP cc_start: 0.8603 (t0) cc_final: 0.8284 (t0) REVERT: C 228 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8597 (mmmm) REVERT: C 376 GLU cc_start: 0.8376 (tp30) cc_final: 0.8085 (tp30) REVERT: C 458 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8405 (ttp80) REVERT: D 20 GLN cc_start: 0.9146 (mt0) cc_final: 0.8678 (mt0) REVERT: D 40 ASP cc_start: 0.8944 (t0) cc_final: 0.8495 (t0) REVERT: D 86 GLU cc_start: 0.8425 (tp30) cc_final: 0.8143 (tm-30) REVERT: D 87 ILE cc_start: 0.9604 (mp) cc_final: 0.9305 (mp) REVERT: D 217 ASP cc_start: 0.8715 (t0) cc_final: 0.8347 (t0) REVERT: D 228 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8581 (mmmm) REVERT: D 452 MET cc_start: 0.9078 (mmp) cc_final: 0.8691 (mmp) REVERT: D 458 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8281 (mtp-110) REVERT: D 461 GLU cc_start: 0.8359 (pm20) cc_final: 0.8110 (pm20) REVERT: D 468 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8442 (mt-10) REVERT: D 501 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8017 (tm-30) REVERT: D 504 ASN cc_start: 0.8429 (m-40) cc_final: 0.8076 (m-40) REVERT: D 523 LYS cc_start: 0.8999 (ptpp) cc_final: 0.8782 (ptpp) REVERT: E 40 ASP cc_start: 0.8882 (t0) cc_final: 0.8136 (t0) REVERT: E 43 ASP cc_start: 0.9106 (m-30) cc_final: 0.8470 (m-30) REVERT: E 206 ASP cc_start: 0.8502 (t70) cc_final: 0.8195 (t0) REVERT: E 217 ASP cc_start: 0.8665 (t0) cc_final: 0.8226 (t0) REVERT: E 228 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8528 (mmmm) REVERT: E 346 SER cc_start: 0.9127 (m) cc_final: 0.8717 (p) REVERT: E 354 MET cc_start: 0.5290 (ptp) cc_final: 0.4096 (tpp) REVERT: E 376 GLU cc_start: 0.8404 (tp30) cc_final: 0.8001 (tp30) REVERT: E 377 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8707 (ttm-80) REVERT: E 458 ARG cc_start: 0.8565 (ttp80) cc_final: 0.8065 (mtp-110) REVERT: E 461 GLU cc_start: 0.8207 (pm20) cc_final: 0.7879 (pm20) REVERT: E 468 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8528 (mt-10) REVERT: E 492 ARG cc_start: 0.7751 (ptp-170) cc_final: 0.7148 (ptp-170) REVERT: E 501 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7976 (tm-30) REVERT: F 20 GLN cc_start: 0.9189 (mt0) cc_final: 0.8847 (mt0) REVERT: F 40 ASP cc_start: 0.8907 (t0) cc_final: 0.8442 (t0) REVERT: F 51 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: F 86 GLU cc_start: 0.6473 (mm-30) cc_final: 0.6207 (mm-30) REVERT: F 110 ASN cc_start: 0.8986 (m-40) cc_final: 0.8756 (m-40) REVERT: F 217 ASP cc_start: 0.8607 (t0) cc_final: 0.8289 (t0) REVERT: F 228 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8615 (mmmm) REVERT: F 346 SER cc_start: 0.9201 (m) cc_final: 0.8598 (p) REVERT: F 376 GLU cc_start: 0.8414 (tp30) cc_final: 0.7947 (tp30) REVERT: F 379 ARG cc_start: 0.9117 (tmm-80) cc_final: 0.8589 (tmm-80) REVERT: F 458 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8270 (ptp-110) REVERT: F 468 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8366 (mt-10) REVERT: F 522 LYS cc_start: 0.9113 (tmtt) cc_final: 0.8907 (tmtt) REVERT: F 523 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9049 (ptpp) REVERT: G 20 GLN cc_start: 0.9145 (mt0) cc_final: 0.8687 (mt0) REVERT: G 40 ASP cc_start: 0.8933 (t0) cc_final: 0.8487 (t0) REVERT: G 66 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8616 (mt-10) REVERT: G 217 ASP cc_start: 0.8726 (t0) cc_final: 0.8352 (t0) REVERT: G 458 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8362 (mtm110) REVERT: G 468 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8653 (mt-10) REVERT: G 485 GLU cc_start: 0.8688 (tp30) cc_final: 0.8483 (tp30) REVERT: G 504 ASN cc_start: 0.8348 (m-40) cc_final: 0.7986 (m-40) REVERT: H 40 ASP cc_start: 0.8877 (t0) cc_final: 0.8127 (t0) REVERT: H 43 ASP cc_start: 0.9116 (m-30) cc_final: 0.8475 (m-30) REVERT: H 217 ASP cc_start: 0.8658 (t0) cc_final: 0.8221 (t0) REVERT: H 228 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8523 (mmmm) REVERT: H 308 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9289 (pp) REVERT: H 346 SER cc_start: 0.9016 (m) cc_final: 0.8534 (p) REVERT: H 354 MET cc_start: 0.5307 (ptp) cc_final: 0.4155 (tpp) REVERT: H 455 TYR cc_start: 0.7889 (m-80) cc_final: 0.7237 (m-80) REVERT: H 458 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8253 (ttp80) REVERT: H 468 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8626 (mt-10) REVERT: H 489 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8966 (tp40) REVERT: H 523 LYS cc_start: 0.9256 (ptpp) cc_final: 0.8880 (pttm) REVERT: I 1 MET cc_start: 0.8065 (ppp) cc_final: 0.7658 (ppp) REVERT: I 20 GLN cc_start: 0.9189 (mt0) cc_final: 0.8797 (mt0) REVERT: I 40 ASP cc_start: 0.8913 (t0) cc_final: 0.8243 (t0) REVERT: I 43 ASP cc_start: 0.9122 (m-30) cc_final: 0.8542 (m-30) REVERT: I 51 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: I 217 ASP cc_start: 0.8607 (t0) cc_final: 0.8291 (t0) REVERT: I 228 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8595 (mmmm) REVERT: I 376 GLU cc_start: 0.8439 (tp30) cc_final: 0.7729 (tp30) REVERT: I 379 ARG cc_start: 0.9111 (tmm-80) cc_final: 0.8674 (tmm-80) REVERT: I 458 ARG cc_start: 0.8549 (ttp80) cc_final: 0.7953 (mtp-110) REVERT: I 461 GLU cc_start: 0.8270 (pm20) cc_final: 0.7595 (pm20) REVERT: I 468 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8421 (mt-10) REVERT: I 485 GLU cc_start: 0.8448 (tp30) cc_final: 0.8217 (tp30) REVERT: I 487 MET cc_start: 0.9494 (mmm) cc_final: 0.9277 (mtp) REVERT: I 513 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8218 (t0) REVERT: I 523 LYS cc_start: 0.9324 (ptpp) cc_final: 0.8954 (pttm) REVERT: J 20 GLN cc_start: 0.9159 (mt0) cc_final: 0.8721 (mt0) REVERT: J 40 ASP cc_start: 0.8951 (t0) cc_final: 0.8470 (t0) REVERT: J 110 ASN cc_start: 0.8753 (m-40) cc_final: 0.7840 (m-40) REVERT: J 217 ASP cc_start: 0.8706 (t0) cc_final: 0.8340 (t0) REVERT: J 228 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8623 (mmmm) REVERT: J 346 SER cc_start: 0.9094 (m) cc_final: 0.8607 (p) REVERT: J 376 GLU cc_start: 0.8191 (tp30) cc_final: 0.7988 (tp30) REVERT: J 426 GLU cc_start: 0.8047 (tt0) cc_final: 0.7777 (tt0) REVERT: J 458 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8273 (ttp80) REVERT: J 468 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8475 (mt-10) REVERT: J 489 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7696 (tp40) REVERT: J 492 ARG cc_start: 0.8316 (ptp-170) cc_final: 0.7692 (ptp-170) REVERT: J 523 LYS cc_start: 0.9087 (ptpp) cc_final: 0.8829 (ptpp) REVERT: K 40 ASP cc_start: 0.8887 (t0) cc_final: 0.8143 (t0) REVERT: K 43 ASP cc_start: 0.9116 (m-30) cc_final: 0.8480 (m-30) REVERT: K 217 ASP cc_start: 0.8664 (t0) cc_final: 0.8232 (t0) REVERT: K 228 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8532 (mmmm) REVERT: K 346 SER cc_start: 0.9167 (m) cc_final: 0.8772 (p) REVERT: K 376 GLU cc_start: 0.8389 (tp30) cc_final: 0.8092 (tp30) REVERT: K 377 ARG cc_start: 0.9321 (ptm-80) cc_final: 0.8938 (ptm-80) REVERT: K 452 MET cc_start: 0.9004 (mmp) cc_final: 0.8555 (mmp) REVERT: K 458 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8333 (mtp-110) REVERT: K 468 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8538 (mt-10) REVERT: L 1 MET cc_start: 0.8187 (ppp) cc_final: 0.7817 (ppp) REVERT: L 20 GLN cc_start: 0.9190 (mt0) cc_final: 0.8851 (mt0) REVERT: L 40 ASP cc_start: 0.8917 (t0) cc_final: 0.8247 (t0) REVERT: L 43 ASP cc_start: 0.9119 (m-30) cc_final: 0.8503 (m-30) REVERT: L 51 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: L 217 ASP cc_start: 0.8605 (t0) cc_final: 0.8286 (t0) REVERT: L 228 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8594 (mmmm) REVERT: L 366 THR cc_start: 0.8982 (m) cc_final: 0.8605 (p) REVERT: L 376 GLU cc_start: 0.8408 (tp30) cc_final: 0.8110 (tp30) REVERT: L 458 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8080 (ttp80) REVERT: L 461 GLU cc_start: 0.8353 (pm20) cc_final: 0.7950 (pm20) REVERT: L 468 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8396 (mt-10) REVERT: L 485 GLU cc_start: 0.8504 (tp30) cc_final: 0.8172 (tp30) REVERT: L 522 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8574 (ttpp) REVERT: L 523 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8742 (ptpp) outliers start: 227 outliers final: 204 residues processed: 1415 average time/residue: 0.6262 time to fit residues: 1440.9329 Evaluate side-chains 1505 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1289 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 458 ARG Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 508 ASP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 57 LYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 377 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 508 ASP Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 377 ARG Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 393 PHE Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 473 LEU Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 492 ARG Chi-restraints excluded: chain F residue 508 ASP Chi-restraints excluded: chain F residue 515 ASP Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 LYS Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 336 LEU Chi-restraints excluded: chain G residue 349 ASP Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 482 LEU Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 515 ASP Chi-restraints excluded: chain G residue 518 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 229 ILE Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 270 MET Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 457 VAL Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 489 GLN Chi-restraints excluded: chain H residue 508 ASP Chi-restraints excluded: chain H residue 515 ASP Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 363 LEU Chi-restraints excluded: chain I residue 377 ARG Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 457 VAL Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 508 ASP Chi-restraints excluded: chain I residue 513 ASN Chi-restraints excluded: chain I residue 515 ASP Chi-restraints excluded: chain I residue 518 LEU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 387 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 515 ASP Chi-restraints excluded: chain J residue 518 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain K residue 227 SER Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 270 MET Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 417 LEU Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 458 ARG Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain K residue 515 ASP Chi-restraints excluded: chain K residue 518 LEU Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 308 ILE Chi-restraints excluded: chain L residue 349 ASP Chi-restraints excluded: chain L residue 377 ARG Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 473 LEU Chi-restraints excluded: chain L residue 482 LEU Chi-restraints excluded: chain L residue 508 ASP Chi-restraints excluded: chain L residue 515 ASP Chi-restraints excluded: chain L residue 518 LEU Chi-restraints excluded: chain L residue 523 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 9.9990 chunk 378 optimal weight: 0.9990 chunk 507 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 438 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 476 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 chunk 489 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN D 526 ASN H 489 GLN H 504 ASN J 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.078712 restraints weight = 98813.953| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.98 r_work: 0.2684 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 49392 Z= 0.183 Angle : 0.609 11.484 66708 Z= 0.322 Chirality : 0.043 0.251 7416 Planarity : 0.003 0.083 8496 Dihedral : 6.218 59.990 6638 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.99 % Favored : 96.81 % Rotamer: Outliers : 3.87 % Allowed : 19.36 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.11), residues: 5928 helix: 2.26 (0.09), residues: 2904 sheet: -0.75 (0.17), residues: 984 loop : 0.13 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 180 HIS 0.002 0.000 HIS G 296 PHE 0.024 0.001 PHE H 161 TYR 0.010 0.001 TYR J 455 ARG 0.011 0.001 ARG F 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20726.94 seconds wall clock time: 364 minutes 2.03 seconds (21842.03 seconds total)