Starting phenix.real_space_refine on Fri Mar 22 19:44:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/03_2024/5ftk_3296_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/03_2024/5ftk_3296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/03_2024/5ftk_3296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/03_2024/5ftk_3296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/03_2024/5ftk_3296_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/03_2024/5ftk_3296_updated.pdb" } resolution = 2.4 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21486 2.51 5 N 6036 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34374 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 681} Chain breaks: 1 Chain: "B" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 681} Chain breaks: 1 Chain: "C" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 681} Chain breaks: 1 Chain: "D" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 681} Chain breaks: 1 Chain: "E" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 681} Chain breaks: 1 Chain: "F" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 681} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 17.13, per 1000 atoms: 0.50 Number of scatterers: 34374 At special positions: 0 Unit cell: (167.531, 176.449, 97.461, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6648 8.00 N 6036 7.00 C 21486 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 - 3.50 Amino acid : False - 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: 12.48 Conformation dependent library (CDL) restraints added in 5.3 seconds 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 42 sheets defined 37.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.843A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 212 through 225 removed outlier: 4.558A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.618A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 282 through 293 removed outlier: 3.579A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.911A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 removed outlier: 4.175A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 402 No H-bonds generated for 'chain 'A' and resid 399 through 402' Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.707A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.520A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.795A pdb=" N ASP A 564 " --> pdb=" O GLU A 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 661 removed outlier: 3.774A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 704 removed outlier: 3.589A pdb=" N GLU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.179A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 762 removed outlier: 3.667A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.843A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 212 through 225 removed outlier: 4.557A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.618A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.578A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.912A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 removed outlier: 4.174A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 402 No H-bonds generated for 'chain 'B' and resid 399 through 402' Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.707A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.520A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.795A pdb=" N ASP B 564 " --> pdb=" O GLU B 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 568 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.773A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 704 removed outlier: 3.589A pdb=" N GLU B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.180A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 removed outlier: 3.666A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.843A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 212 through 225 removed outlier: 4.557A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.618A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 282 through 293 removed outlier: 3.579A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.911A pdb=" N GLN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 removed outlier: 4.175A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 402 No H-bonds generated for 'chain 'C' and resid 399 through 402' Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.707A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 removed outlier: 3.521A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.794A pdb=" N ASP C 564 " --> pdb=" O GLU C 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 568 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.774A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 704 removed outlier: 3.589A pdb=" N GLU C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.180A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 762 removed outlier: 3.667A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.843A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 212 through 225 removed outlier: 4.558A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.618A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 282 through 293 removed outlier: 3.579A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 332 removed outlier: 3.912A pdb=" N GLN D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 removed outlier: 4.174A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 402 No H-bonds generated for 'chain 'D' and resid 399 through 402' Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.707A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 456 removed outlier: 3.520A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.795A pdb=" N ASP D 564 " --> pdb=" O GLU D 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 568 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.773A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 704 removed outlier: 3.590A pdb=" N GLU D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.179A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 762 removed outlier: 3.667A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.843A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 212 through 225 removed outlier: 4.558A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.617A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 282 through 293 removed outlier: 3.578A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 332 removed outlier: 3.911A pdb=" N GLN E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 328 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 removed outlier: 4.174A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 402 No H-bonds generated for 'chain 'E' and resid 399 through 402' Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.707A pdb=" N ASN E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 456 removed outlier: 3.521A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.795A pdb=" N ASP E 564 " --> pdb=" O GLU E 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN E 568 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 661 removed outlier: 3.773A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 704 removed outlier: 3.590A pdb=" N GLU E 704 " --> pdb=" O ARG E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 742 removed outlier: 4.180A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 762 removed outlier: 3.667A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 removed outlier: 3.843A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 134 No H-bonds generated for 'chain 'F' and resid 131 through 134' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 212 through 225 removed outlier: 4.558A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.618A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 282 through 293 removed outlier: 3.579A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 332 removed outlier: 3.911A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 removed outlier: 4.175A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 402 No H-bonds generated for 'chain 'F' and resid 399 through 402' Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.707A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 456 removed outlier: 3.521A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.796A pdb=" N ASP F 564 " --> pdb=" O GLU F 561 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN F 568 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 661 removed outlier: 3.773A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 704 removed outlier: 3.589A pdb=" N GLU F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 742 removed outlier: 4.180A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 removed outlier: 3.666A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 42 removed outlier: 6.420A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU A 41 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 72 " --> pdb=" O LEU A 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 65 through 69 Processing sheet with id= D, first strand: chain 'A' and resid 153 through 156 Processing sheet with id= E, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.547A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 642 through 644 removed outlier: 8.112A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 115 through 118 removed outlier: 3.532A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= I, first strand: chain 'B' and resid 38 through 42 removed outlier: 6.420A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 65 through 69 Processing sheet with id= K, first strand: chain 'B' and resid 153 through 156 Processing sheet with id= L, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.547A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 642 through 644 removed outlier: 8.112A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.532A pdb=" N GLU B 167 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 99 through 101 Processing sheet with id= P, first strand: chain 'C' and resid 38 through 42 removed outlier: 6.421A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= R, first strand: chain 'C' and resid 153 through 156 Processing sheet with id= S, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.546A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 642 through 644 removed outlier: 8.111A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 115 through 118 removed outlier: 3.532A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= W, first strand: chain 'D' and resid 38 through 42 removed outlier: 6.420A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 65 through 69 Processing sheet with id= Y, first strand: chain 'D' and resid 153 through 156 Processing sheet with id= Z, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.547A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 642 through 644 removed outlier: 8.111A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 115 through 118 removed outlier: 3.533A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= AD, first strand: chain 'E' and resid 38 through 42 removed outlier: 6.420A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 65 through 69 Processing sheet with id= AF, first strand: chain 'E' and resid 153 through 156 Processing sheet with id= AG, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.546A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 642 through 644 removed outlier: 8.111A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'E' and resid 115 through 118 removed outlier: 3.532A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= AK, first strand: chain 'F' and resid 38 through 42 removed outlier: 6.421A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'F' and resid 65 through 69 Processing sheet with id= AM, first strand: chain 'F' and resid 153 through 156 Processing sheet with id= AN, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.547A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 642 through 644 removed outlier: 8.112A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'F' and resid 115 through 118 removed outlier: 3.532A pdb=" N GLU F 167 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2502 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: 13.30 Time building geometry restraints manager: 13.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10389 1.33 - 1.45: 5517 1.45 - 1.58: 18618 1.58 - 1.70: 42 1.70 - 1.82: 288 Bond restraints: 34854 Sorted by residual: bond pdb=" CB VAL A 367 " pdb=" CG1 VAL A 367 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.69e+00 bond pdb=" CB VAL F 367 " pdb=" CG1 VAL F 367 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.69e+00 bond pdb=" CB VAL C 367 " pdb=" CG1 VAL C 367 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.69e+00 bond pdb=" CB VAL E 367 " pdb=" CG1 VAL E 367 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.67e+00 bond pdb=" CB VAL D 367 " pdb=" CG1 VAL D 367 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.67e+00 ... (remaining 34849 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.36: 955 105.36 - 113.10: 18718 113.10 - 120.83: 16729 120.83 - 128.56: 10526 128.56 - 136.30: 214 Bond angle restraints: 47142 Sorted by residual: angle pdb=" N THR C 122 " pdb=" CA THR C 122 " pdb=" C THR C 122 " ideal model delta sigma weight residual 112.92 127.22 -14.30 1.23e+00 6.61e-01 1.35e+02 angle pdb=" N THR F 122 " pdb=" CA THR F 122 " pdb=" C THR F 122 " ideal model delta sigma weight residual 112.92 127.20 -14.28 1.23e+00 6.61e-01 1.35e+02 angle pdb=" N THR D 122 " pdb=" CA THR D 122 " pdb=" C THR D 122 " ideal model delta sigma weight residual 112.92 127.19 -14.27 1.23e+00 6.61e-01 1.35e+02 angle pdb=" N THR A 122 " pdb=" CA THR A 122 " pdb=" C THR A 122 " ideal model delta sigma weight residual 112.92 127.18 -14.26 1.23e+00 6.61e-01 1.34e+02 angle pdb=" N THR E 122 " pdb=" CA THR E 122 " pdb=" C THR E 122 " ideal model delta sigma weight residual 112.92 127.17 -14.25 1.23e+00 6.61e-01 1.34e+02 ... (remaining 47137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.99: 20985 24.99 - 49.98: 519 49.98 - 74.98: 36 74.98 - 99.97: 36 99.97 - 124.96: 6 Dihedral angle restraints: 21582 sinusoidal: 9090 harmonic: 12492 Sorted by residual: dihedral pdb=" CA ARG E 210 " pdb=" C ARG E 210 " pdb=" N LYS E 211 " pdb=" CA LYS E 211 " ideal model delta harmonic sigma weight residual 180.00 140.91 39.09 0 5.00e+00 4.00e-02 6.11e+01 dihedral pdb=" CA ARG A 210 " pdb=" C ARG A 210 " pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta harmonic sigma weight residual 180.00 140.95 39.05 0 5.00e+00 4.00e-02 6.10e+01 dihedral pdb=" CA ARG D 210 " pdb=" C ARG D 210 " pdb=" N LYS D 211 " pdb=" CA LYS D 211 " ideal model delta harmonic sigma weight residual 180.00 140.95 39.05 0 5.00e+00 4.00e-02 6.10e+01 ... (remaining 21579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3294 0.057 - 0.113: 1488 0.113 - 0.170: 427 0.170 - 0.226: 76 0.226 - 0.283: 31 Chirality restraints: 5316 Sorted by residual: chirality pdb=" CA THR E 122 " pdb=" N THR E 122 " pdb=" C THR E 122 " pdb=" CB THR E 122 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA THR C 122 " pdb=" N THR C 122 " pdb=" C THR C 122 " pdb=" CB THR C 122 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA THR A 122 " pdb=" N THR A 122 " pdb=" C THR A 122 " pdb=" CB THR A 122 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 5313 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 225 " -0.494 9.50e-02 1.11e+02 2.21e-01 2.98e+01 pdb=" NE ARG E 225 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG E 225 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 225 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 225 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 225 " -0.493 9.50e-02 1.11e+02 2.21e-01 2.97e+01 pdb=" NE ARG C 225 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG C 225 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 225 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 225 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 225 " -0.492 9.50e-02 1.11e+02 2.21e-01 2.97e+01 pdb=" NE ARG A 225 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 225 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 225 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 225 " -0.017 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 6137 2.75 - 3.29: 36109 3.29 - 3.83: 57304 3.83 - 4.36: 72057 4.36 - 4.90: 111882 Nonbonded interactions: 283489 Sorted by model distance: nonbonded pdb=" NH2 ARG A 53 " pdb=" OG SER A 73 " model vdw 2.216 2.520 nonbonded pdb=" NH2 ARG D 53 " pdb=" OG SER D 73 " model vdw 2.217 2.520 nonbonded pdb=" NH2 ARG F 53 " pdb=" OG SER F 73 " model vdw 2.217 2.520 nonbonded pdb=" NH2 ARG E 53 " pdb=" OG SER E 73 " model vdw 2.217 2.520 nonbonded pdb=" NH2 ARG B 53 " pdb=" OG SER B 73 " model vdw 2.217 2.520 ... (remaining 283484 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.030 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 87.180 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.260 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 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 : 0.011 0.092 34854 Z= 0.751 Angle : 1.387 14.301 47142 Z= 0.797 Chirality : 0.070 0.283 5316 Planarity : 0.011 0.221 6186 Dihedral : 12.311 124.961 13482 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.12 % Favored : 93.46 % Rotamer: Outliers : 0.65 % Allowed : 2.47 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.37 (0.09), residues: 4314 helix: -3.50 (0.08), residues: 1560 sheet: -2.10 (0.15), residues: 678 loop : -2.60 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP F 551 HIS 0.015 0.003 HIS D 406 PHE 0.067 0.007 PHE B 563 TYR 0.039 0.006 TYR D 755 ARG 0.017 0.002 ARG F 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 905 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.5270 (m-40) cc_final: 0.4852 (m110) REVERT: A 46 MET cc_start: 0.2692 (mmt) cc_final: 0.2409 (mmm) REVERT: A 56 THR cc_start: 0.5790 (p) cc_final: 0.4999 (m) REVERT: A 57 VAL cc_start: 0.5716 (t) cc_final: 0.5502 (p) REVERT: A 60 LYS cc_start: 0.4751 (mmtm) cc_final: 0.4248 (mppt) REVERT: A 110 TYR cc_start: 0.3803 (m-10) cc_final: 0.3415 (m-10) REVERT: A 122 THR cc_start: 0.5948 (p) cc_final: 0.5314 (t) REVERT: A 288 LYS cc_start: 0.6892 (ttpp) cc_final: 0.6649 (pttp) REVERT: A 317 HIS cc_start: 0.4912 (m90) cc_final: 0.4682 (t-90) REVERT: A 322 ARG cc_start: 0.6635 (mtt90) cc_final: 0.6422 (mtt90) REVERT: A 354 ASP cc_start: 0.6624 (t70) cc_final: 0.6066 (t70) REVERT: A 377 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7113 (mtm-85) REVERT: A 379 GLU cc_start: 0.7383 (mp0) cc_final: 0.7158 (mp0) REVERT: A 401 ASN cc_start: 0.5920 (m110) cc_final: 0.5497 (m110) REVERT: A 402 GLU cc_start: 0.6057 (mp0) cc_final: 0.5688 (tp30) REVERT: A 449 MET cc_start: 0.6655 (tpt) cc_final: 0.6444 (tpt) REVERT: A 487 ARG cc_start: 0.6629 (ttp-110) cc_final: 0.6360 (ptp90) REVERT: A 491 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 505 LYS cc_start: 0.6002 (mtpt) cc_final: 0.5730 (tppp) REVERT: A 546 GLU cc_start: 0.8097 (tt0) cc_final: 0.7433 (mt-10) REVERT: A 624 ASN cc_start: 0.7855 (p0) cc_final: 0.7641 (m-40) REVERT: A 653 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.7025 (mtp180) REVERT: A 696 LYS cc_start: 0.7435 (tttp) cc_final: 0.7164 (ttpt) REVERT: A 738 GLU cc_start: 0.5123 (mm-30) cc_final: 0.4908 (mm-30) REVERT: B 26 LEU cc_start: 0.5024 (tp) cc_final: 0.4823 (mt) REVERT: B 36 ASN cc_start: 0.5349 (m-40) cc_final: 0.5038 (m-40) REVERT: B 57 VAL cc_start: 0.5711 (t) cc_final: 0.5490 (p) REVERT: B 60 LYS cc_start: 0.4805 (mmtm) cc_final: 0.4297 (mppt) REVERT: B 174 CYS cc_start: 0.4541 (m) cc_final: 0.4094 (p) REVERT: B 288 LYS cc_start: 0.6775 (ttpp) cc_final: 0.6566 (pttp) REVERT: B 305 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 386 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6601 (mmtm) REVERT: B 401 ASN cc_start: 0.5993 (m110) cc_final: 0.5589 (m110) REVERT: B 402 GLU cc_start: 0.6133 (mp0) cc_final: 0.5697 (tp30) REVERT: B 449 MET cc_start: 0.6667 (tpt) cc_final: 0.6442 (tpt) REVERT: B 491 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6662 (mt-10) REVERT: B 546 GLU cc_start: 0.8109 (tt0) cc_final: 0.7477 (mt-10) REVERT: B 590 ILE cc_start: 0.2565 (OUTLIER) cc_final: 0.2362 (tt) REVERT: B 624 ASN cc_start: 0.7844 (p0) cc_final: 0.7585 (m-40) REVERT: B 696 LYS cc_start: 0.7476 (tttp) cc_final: 0.7228 (ttpt) REVERT: B 733 ARG cc_start: 0.4302 (ttt180) cc_final: 0.3595 (ttp-170) REVERT: C 36 ASN cc_start: 0.5230 (m-40) cc_final: 0.4729 (m110) REVERT: C 46 MET cc_start: 0.2572 (mmt) cc_final: 0.2329 (mmm) REVERT: C 60 LYS cc_start: 0.4811 (mmtm) cc_final: 0.4289 (mppt) REVERT: C 101 SER cc_start: 0.4735 (t) cc_final: 0.4509 (m) REVERT: C 110 TYR cc_start: 0.4001 (m-10) cc_final: 0.3705 (m-10) REVERT: C 122 THR cc_start: 0.5854 (p) cc_final: 0.5242 (t) REVERT: C 174 CYS cc_start: 0.4561 (m) cc_final: 0.4140 (p) REVERT: C 291 GLU cc_start: 0.5850 (tm-30) cc_final: 0.4930 (tm-30) REVERT: C 377 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.6968 (mtm180) REVERT: C 386 LYS cc_start: 0.7163 (mtpt) cc_final: 0.6550 (mmtm) REVERT: C 401 ASN cc_start: 0.5966 (m110) cc_final: 0.5607 (m110) REVERT: C 402 GLU cc_start: 0.6122 (mp0) cc_final: 0.5814 (tp30) REVERT: C 491 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6585 (mt-10) REVERT: C 505 LYS cc_start: 0.6000 (mtpt) cc_final: 0.5720 (tppp) REVERT: C 546 GLU cc_start: 0.8165 (tt0) cc_final: 0.7580 (mt-10) REVERT: C 624 ASN cc_start: 0.7862 (p0) cc_final: 0.7637 (p0) REVERT: C 696 LYS cc_start: 0.7461 (tttp) cc_final: 0.7186 (ttpt) REVERT: D 36 ASN cc_start: 0.5314 (m-40) cc_final: 0.4892 (m110) REVERT: D 46 MET cc_start: 0.2686 (mmt) cc_final: 0.2412 (mmm) REVERT: D 56 THR cc_start: 0.5794 (p) cc_final: 0.4981 (m) REVERT: D 57 VAL cc_start: 0.5703 (t) cc_final: 0.5477 (p) REVERT: D 60 LYS cc_start: 0.4734 (mmtm) cc_final: 0.4243 (mppt) REVERT: D 110 TYR cc_start: 0.3835 (m-10) cc_final: 0.3440 (m-10) REVERT: D 122 THR cc_start: 0.5944 (p) cc_final: 0.5314 (t) REVERT: D 288 LYS cc_start: 0.6876 (ttpp) cc_final: 0.6646 (pttp) REVERT: D 322 ARG cc_start: 0.6621 (mtt90) cc_final: 0.6420 (mtt90) REVERT: D 354 ASP cc_start: 0.6628 (t70) cc_final: 0.6104 (t70) REVERT: D 377 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.7121 (mtm-85) REVERT: D 379 GLU cc_start: 0.7381 (mp0) cc_final: 0.7156 (mp0) REVERT: D 401 ASN cc_start: 0.5949 (m110) cc_final: 0.5529 (m110) REVERT: D 402 GLU cc_start: 0.6031 (mp0) cc_final: 0.5662 (tp30) REVERT: D 449 MET cc_start: 0.6648 (tpt) cc_final: 0.6440 (tpt) REVERT: D 487 ARG cc_start: 0.6643 (ttp-110) cc_final: 0.6366 (ptp90) REVERT: D 491 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6701 (mt-10) REVERT: D 505 LYS cc_start: 0.5995 (mtpt) cc_final: 0.5728 (tppp) REVERT: D 546 GLU cc_start: 0.8089 (tt0) cc_final: 0.7454 (mt-10) REVERT: D 624 ASN cc_start: 0.7841 (p0) cc_final: 0.7636 (m-40) REVERT: D 653 ARG cc_start: 0.7255 (mtm-85) cc_final: 0.7040 (mtp180) REVERT: D 696 LYS cc_start: 0.7456 (tttp) cc_final: 0.7174 (ttpt) REVERT: D 738 GLU cc_start: 0.5113 (mm-30) cc_final: 0.4883 (mm-30) REVERT: E 26 LEU cc_start: 0.5025 (tp) cc_final: 0.4820 (mt) REVERT: E 36 ASN cc_start: 0.5375 (m-40) cc_final: 0.4914 (m110) REVERT: E 57 VAL cc_start: 0.5672 (t) cc_final: 0.5452 (p) REVERT: E 60 LYS cc_start: 0.4822 (mmtm) cc_final: 0.4311 (mppt) REVERT: E 110 TYR cc_start: 0.3729 (m-10) cc_final: 0.3478 (m-10) REVERT: E 174 CYS cc_start: 0.4516 (m) cc_final: 0.4045 (p) REVERT: E 288 LYS cc_start: 0.6777 (ttpp) cc_final: 0.6569 (pttp) REVERT: E 305 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7292 (mt-10) REVERT: E 386 LYS cc_start: 0.7190 (mtpt) cc_final: 0.6586 (mmtm) REVERT: E 401 ASN cc_start: 0.5993 (m110) cc_final: 0.5603 (m110) REVERT: E 402 GLU cc_start: 0.6154 (mp0) cc_final: 0.5692 (tp30) REVERT: E 491 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6676 (mt-10) REVERT: E 546 GLU cc_start: 0.8112 (tt0) cc_final: 0.7480 (mt-10) REVERT: E 590 ILE cc_start: 0.2579 (OUTLIER) cc_final: 0.2366 (tt) REVERT: E 624 ASN cc_start: 0.7845 (p0) cc_final: 0.7584 (m-40) REVERT: E 696 LYS cc_start: 0.7488 (tttp) cc_final: 0.7244 (ttpt) REVERT: E 733 ARG cc_start: 0.4357 (ttt180) cc_final: 0.3640 (ttp-170) REVERT: F 36 ASN cc_start: 0.5243 (m-40) cc_final: 0.4745 (m110) REVERT: F 46 MET cc_start: 0.2587 (mmt) cc_final: 0.2343 (mmm) REVERT: F 60 LYS cc_start: 0.4824 (mmtm) cc_final: 0.4295 (mppt) REVERT: F 101 SER cc_start: 0.4737 (t) cc_final: 0.4510 (m) REVERT: F 110 TYR cc_start: 0.3996 (m-10) cc_final: 0.3701 (m-10) REVERT: F 122 THR cc_start: 0.5825 (p) cc_final: 0.5232 (t) REVERT: F 174 CYS cc_start: 0.4551 (m) cc_final: 0.4146 (p) REVERT: F 291 GLU cc_start: 0.5851 (tm-30) cc_final: 0.4931 (tm-30) REVERT: F 377 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.6956 (mtm180) REVERT: F 386 LYS cc_start: 0.7160 (mtpt) cc_final: 0.6547 (mmtm) REVERT: F 401 ASN cc_start: 0.5967 (m110) cc_final: 0.5607 (m110) REVERT: F 402 GLU cc_start: 0.6119 (mp0) cc_final: 0.5811 (tp30) REVERT: F 491 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6592 (mt-10) REVERT: F 505 LYS cc_start: 0.6004 (mtpt) cc_final: 0.5725 (tppp) REVERT: F 546 GLU cc_start: 0.8164 (tt0) cc_final: 0.7579 (mt-10) REVERT: F 624 ASN cc_start: 0.7861 (p0) cc_final: 0.7636 (p0) REVERT: F 696 LYS cc_start: 0.7460 (tttp) cc_final: 0.7185 (ttpt) outliers start: 24 outliers final: 6 residues processed: 929 average time/residue: 1.6881 time to fit residues: 1828.5305 Evaluate side-chains 535 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 527 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 205 optimal weight: 0.0770 chunk 252 optimal weight: 5.9990 chunk 392 optimal weight: 6.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 558 ASN A 568 GLN A 616 ASN B 129 ASN B 285 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 558 ASN B 568 GLN B 616 ASN B 692 GLN B 750 ASN C 129 ASN C 285 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN C 616 ASN C 692 GLN C 750 ASN D 129 ASN D 285 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 558 ASN D 568 GLN D 616 ASN E 129 ASN E 285 ASN E 536 GLN E 558 ASN E 568 GLN E 616 ASN E 692 GLN E 750 ASN F 129 ASN F 285 ASN F 317 HIS ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN F 616 ASN F 692 GLN F 750 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34854 Z= 0.272 Angle : 0.806 14.079 47142 Z= 0.407 Chirality : 0.049 0.166 5316 Planarity : 0.006 0.057 6186 Dihedral : 8.868 102.430 4846 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.31 % Allowed : 13.33 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.03 (0.11), residues: 4314 helix: -1.91 (0.11), residues: 1608 sheet: -1.62 (0.17), residues: 726 loop : -2.15 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 551 HIS 0.005 0.001 HIS B 406 PHE 0.017 0.002 PHE E 139 TYR 0.019 0.002 TYR E 755 ARG 0.011 0.001 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 603 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.5546 (m-40) cc_final: 0.5190 (m110) REVERT: A 46 MET cc_start: 0.2626 (mmt) cc_final: 0.2424 (pmm) REVERT: A 56 THR cc_start: 0.5683 (p) cc_final: 0.4930 (m) REVERT: A 82 ILE cc_start: 0.5135 (OUTLIER) cc_final: 0.4810 (pp) REVERT: A 110 TYR cc_start: 0.3709 (m-10) cc_final: 0.3287 (m-10) REVERT: A 377 ARG cc_start: 0.7404 (mtm-85) cc_final: 0.7194 (mtm180) REVERT: A 378 LEU cc_start: 0.7308 (tm) cc_final: 0.6891 (tp) REVERT: A 379 GLU cc_start: 0.7082 (mp0) cc_final: 0.6865 (mp0) REVERT: A 401 ASN cc_start: 0.6188 (m110) cc_final: 0.5780 (m-40) REVERT: A 402 GLU cc_start: 0.5944 (mp0) cc_final: 0.5711 (tp30) REVERT: A 426 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5817 (mtmt) REVERT: A 460 ASN cc_start: 0.5124 (OUTLIER) cc_final: 0.4727 (p0) REVERT: A 491 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6703 (mt-10) REVERT: A 505 LYS cc_start: 0.5992 (mtpt) cc_final: 0.5708 (tppp) REVERT: A 546 GLU cc_start: 0.7971 (tt0) cc_final: 0.7483 (mt-10) REVERT: A 650 GLU cc_start: 0.5972 (pm20) cc_final: 0.5721 (tt0) REVERT: A 696 LYS cc_start: 0.7332 (tttp) cc_final: 0.7002 (ttpt) REVERT: A 732 ARG cc_start: 0.4692 (mtm-85) cc_final: 0.4449 (mtm180) REVERT: A 738 GLU cc_start: 0.5211 (mm-30) cc_final: 0.4998 (mm-30) REVERT: A 758 PHE cc_start: 0.6052 (t80) cc_final: 0.5828 (t80) REVERT: B 36 ASN cc_start: 0.5403 (m-40) cc_final: 0.5054 (m110) REVERT: B 56 THR cc_start: 0.5668 (p) cc_final: 0.4971 (m) REVERT: B 57 VAL cc_start: 0.5483 (t) cc_final: 0.5130 (p) REVERT: B 82 ILE cc_start: 0.5054 (pt) cc_final: 0.4783 (pp) REVERT: B 288 LYS cc_start: 0.6586 (ttpp) cc_final: 0.6365 (pttp) REVERT: B 292 GLU cc_start: 0.6416 (tm-30) cc_final: 0.6211 (tm-30) REVERT: B 322 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.5825 (mmt90) REVERT: B 378 LEU cc_start: 0.7270 (tm) cc_final: 0.6960 (tp) REVERT: B 401 ASN cc_start: 0.6107 (m110) cc_final: 0.5628 (m-40) REVERT: B 402 GLU cc_start: 0.5995 (mp0) cc_final: 0.5641 (tp30) REVERT: B 425 LYS cc_start: 0.6344 (mtmt) cc_final: 0.6134 (ttmt) REVERT: B 426 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6033 (mtmt) REVERT: B 449 MET cc_start: 0.6621 (tpt) cc_final: 0.6323 (tpt) REVERT: B 460 ASN cc_start: 0.5140 (OUTLIER) cc_final: 0.4821 (p0) REVERT: B 478 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6872 (m-30) REVERT: B 491 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6686 (mt-10) REVERT: B 546 GLU cc_start: 0.8028 (tt0) cc_final: 0.7600 (mt-10) REVERT: B 624 ASN cc_start: 0.7805 (p0) cc_final: 0.7555 (m110) REVERT: B 650 GLU cc_start: 0.6019 (pm20) cc_final: 0.5767 (pm20) REVERT: B 696 LYS cc_start: 0.7370 (tttp) cc_final: 0.7110 (ttpt) REVERT: B 732 ARG cc_start: 0.4788 (mtm-85) cc_final: 0.4538 (mtm180) REVERT: B 733 ARG cc_start: 0.4053 (ttt180) cc_final: 0.3366 (ttp-170) REVERT: C 36 ASN cc_start: 0.5308 (m-40) cc_final: 0.4970 (m110) REVERT: C 56 THR cc_start: 0.5728 (p) cc_final: 0.4996 (m) REVERT: C 60 LYS cc_start: 0.4799 (mmtm) cc_final: 0.4364 (mppt) REVERT: C 82 ILE cc_start: 0.5133 (OUTLIER) cc_final: 0.4809 (pp) REVERT: C 101 SER cc_start: 0.4499 (t) cc_final: 0.4199 (m) REVERT: C 110 TYR cc_start: 0.3882 (m-10) cc_final: 0.3602 (m-10) REVERT: C 292 GLU cc_start: 0.6395 (tm-30) cc_final: 0.6015 (mt-10) REVERT: C 321 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5978 (mp0) REVERT: C 322 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.5858 (mmt90) REVERT: C 377 ARG cc_start: 0.7346 (mtm-85) cc_final: 0.7101 (mtm-85) REVERT: C 401 ASN cc_start: 0.6116 (m110) cc_final: 0.5732 (m110) REVERT: C 402 GLU cc_start: 0.5945 (mp0) cc_final: 0.5736 (tp30) REVERT: C 426 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.5923 (mtmt) REVERT: C 491 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6736 (mt-10) REVERT: C 505 LYS cc_start: 0.5979 (mtpt) cc_final: 0.5663 (tppp) REVERT: C 546 GLU cc_start: 0.8032 (tt0) cc_final: 0.7572 (mt-10) REVERT: C 561 GLU cc_start: 0.7373 (mp0) cc_final: 0.7030 (mp0) REVERT: C 624 ASN cc_start: 0.7777 (p0) cc_final: 0.7575 (m110) REVERT: C 650 GLU cc_start: 0.5954 (pm20) cc_final: 0.5641 (pm20) REVERT: C 696 LYS cc_start: 0.7386 (tttp) cc_final: 0.7125 (ttpt) REVERT: C 732 ARG cc_start: 0.4705 (mtm-85) cc_final: 0.4310 (mtm180) REVERT: C 733 ARG cc_start: 0.4157 (ttt180) cc_final: 0.3452 (ttp-170) REVERT: D 36 ASN cc_start: 0.5538 (m-40) cc_final: 0.5179 (m110) REVERT: D 56 THR cc_start: 0.5729 (p) cc_final: 0.4963 (m) REVERT: D 82 ILE cc_start: 0.5127 (OUTLIER) cc_final: 0.4796 (pp) REVERT: D 110 TYR cc_start: 0.3746 (m-10) cc_final: 0.3316 (m-10) REVERT: D 377 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.7192 (mtm180) REVERT: D 378 LEU cc_start: 0.7295 (tm) cc_final: 0.6873 (tp) REVERT: D 379 GLU cc_start: 0.7093 (mp0) cc_final: 0.6869 (mp0) REVERT: D 401 ASN cc_start: 0.6190 (m110) cc_final: 0.5781 (m-40) REVERT: D 402 GLU cc_start: 0.5948 (mp0) cc_final: 0.5705 (tp30) REVERT: D 460 ASN cc_start: 0.5111 (OUTLIER) cc_final: 0.4714 (p0) REVERT: D 491 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6696 (mt-10) REVERT: D 505 LYS cc_start: 0.5996 (mtpt) cc_final: 0.5707 (tppp) REVERT: D 546 GLU cc_start: 0.7969 (tt0) cc_final: 0.7482 (mt-10) REVERT: D 650 GLU cc_start: 0.5936 (pm20) cc_final: 0.5677 (tt0) REVERT: D 696 LYS cc_start: 0.7341 (tttp) cc_final: 0.7001 (ttpt) REVERT: D 732 ARG cc_start: 0.4703 (mtm-85) cc_final: 0.4456 (mtm180) REVERT: D 738 GLU cc_start: 0.5188 (mm-30) cc_final: 0.4972 (mm-30) REVERT: D 758 PHE cc_start: 0.6040 (t80) cc_final: 0.5810 (t80) REVERT: E 36 ASN cc_start: 0.5396 (m-40) cc_final: 0.5017 (m110) REVERT: E 56 THR cc_start: 0.5657 (p) cc_final: 0.4961 (m) REVERT: E 57 VAL cc_start: 0.5527 (t) cc_final: 0.5184 (p) REVERT: E 60 LYS cc_start: 0.4871 (mmtm) cc_final: 0.4661 (mmtm) REVERT: E 82 ILE cc_start: 0.5035 (pt) cc_final: 0.4766 (pp) REVERT: E 110 TYR cc_start: 0.3750 (m-10) cc_final: 0.3446 (m-10) REVERT: E 288 LYS cc_start: 0.6536 (ttpp) cc_final: 0.6317 (pttp) REVERT: E 292 GLU cc_start: 0.6225 (tm-30) cc_final: 0.5958 (tm-30) REVERT: E 322 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.5818 (mmt90) REVERT: E 378 LEU cc_start: 0.7256 (tm) cc_final: 0.6952 (tp) REVERT: E 401 ASN cc_start: 0.6122 (m110) cc_final: 0.5655 (m-40) REVERT: E 402 GLU cc_start: 0.6002 (mp0) cc_final: 0.5615 (tp30) REVERT: E 426 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6021 (mtmt) REVERT: E 460 ASN cc_start: 0.5166 (OUTLIER) cc_final: 0.4855 (p0) REVERT: E 478 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6878 (m-30) REVERT: E 491 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6713 (mt-10) REVERT: E 546 GLU cc_start: 0.8030 (tt0) cc_final: 0.7601 (mt-10) REVERT: E 624 ASN cc_start: 0.7805 (p0) cc_final: 0.7554 (m110) REVERT: E 650 GLU cc_start: 0.6011 (pm20) cc_final: 0.5749 (pm20) REVERT: E 696 LYS cc_start: 0.7421 (tttp) cc_final: 0.7148 (ttpt) REVERT: E 733 ARG cc_start: 0.4061 (ttt180) cc_final: 0.3339 (ttp-170) REVERT: F 36 ASN cc_start: 0.5306 (m-40) cc_final: 0.4971 (m110) REVERT: F 56 THR cc_start: 0.5729 (p) cc_final: 0.4998 (m) REVERT: F 60 LYS cc_start: 0.4798 (mmtm) cc_final: 0.4367 (mppt) REVERT: F 82 ILE cc_start: 0.5141 (OUTLIER) cc_final: 0.4810 (pp) REVERT: F 101 SER cc_start: 0.4494 (t) cc_final: 0.4198 (m) REVERT: F 110 TYR cc_start: 0.3881 (m-10) cc_final: 0.3601 (m-10) REVERT: F 292 GLU cc_start: 0.6394 (tm-30) cc_final: 0.6014 (mt-10) REVERT: F 321 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5944 (mp0) REVERT: F 322 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5853 (mmt90) REVERT: F 377 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.7082 (mtm-85) REVERT: F 401 ASN cc_start: 0.6117 (m110) cc_final: 0.5730 (m110) REVERT: F 402 GLU cc_start: 0.5941 (mp0) cc_final: 0.5734 (tp30) REVERT: F 426 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.5924 (mtmt) REVERT: F 505 LYS cc_start: 0.5987 (mtpt) cc_final: 0.5666 (tppp) REVERT: F 546 GLU cc_start: 0.8033 (tt0) cc_final: 0.7573 (mt-10) REVERT: F 561 GLU cc_start: 0.7370 (mp0) cc_final: 0.7029 (mp0) REVERT: F 624 ASN cc_start: 0.7777 (p0) cc_final: 0.7574 (m110) REVERT: F 650 GLU cc_start: 0.5951 (pm20) cc_final: 0.5639 (pm20) REVERT: F 696 LYS cc_start: 0.7390 (tttp) cc_final: 0.7128 (ttpt) REVERT: F 732 ARG cc_start: 0.4702 (mtm-85) cc_final: 0.4306 (mtm180) REVERT: F 733 ARG cc_start: 0.4156 (ttt180) cc_final: 0.3449 (ttp-170) outliers start: 122 outliers final: 43 residues processed: 697 average time/residue: 1.6584 time to fit residues: 1353.0774 Evaluate side-chains 583 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 519 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 749 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 326 optimal weight: 30.0000 chunk 267 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 350 optimal weight: 10.0000 chunk 389 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 315 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN A 616 ASN A 624 ASN A 750 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN C 616 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN D 616 ASN D 624 ASN D 750 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN F 317 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN F 616 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34854 Z= 0.318 Angle : 0.802 11.781 47142 Z= 0.401 Chirality : 0.048 0.173 5316 Planarity : 0.006 0.055 6186 Dihedral : 8.587 94.199 4840 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.79 % Favored : 93.07 % Rotamer: Outliers : 4.17 % Allowed : 15.88 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.60 (0.11), residues: 4314 helix: -1.41 (0.11), residues: 1608 sheet: -1.31 (0.18), residues: 684 loop : -2.08 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 551 HIS 0.005 0.002 HIS E 735 PHE 0.017 0.002 PHE E 139 TYR 0.014 0.002 TYR E 755 ARG 0.012 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 555 time to evaluate : 3.739 Fit side-chains REVERT: A 36 ASN cc_start: 0.5457 (m-40) cc_final: 0.5228 (m110) REVERT: A 53 ARG cc_start: 0.3992 (ttm110) cc_final: 0.3623 (ptp90) REVERT: A 56 THR cc_start: 0.5765 (p) cc_final: 0.4941 (m) REVERT: A 82 ILE cc_start: 0.5126 (OUTLIER) cc_final: 0.4796 (pp) REVERT: A 110 TYR cc_start: 0.3751 (m-10) cc_final: 0.3288 (m-10) REVERT: A 291 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5448 (tm-30) REVERT: A 322 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5768 (mmt90) REVERT: A 378 LEU cc_start: 0.7374 (tm) cc_final: 0.6968 (tp) REVERT: A 379 GLU cc_start: 0.6960 (mp0) cc_final: 0.6751 (mp0) REVERT: A 401 ASN cc_start: 0.6146 (m110) cc_final: 0.5708 (m-40) REVERT: A 402 GLU cc_start: 0.6095 (mp0) cc_final: 0.5832 (tp30) REVERT: A 426 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.5732 (mtmt) REVERT: A 460 ASN cc_start: 0.5301 (OUTLIER) cc_final: 0.4903 (p0) REVERT: A 473 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6373 (mm110) REVERT: A 478 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: A 491 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6616 (mt-10) REVERT: A 505 LYS cc_start: 0.5956 (mtpt) cc_final: 0.5649 (tppp) REVERT: A 546 GLU cc_start: 0.7921 (tt0) cc_final: 0.7472 (mt-10) REVERT: A 561 GLU cc_start: 0.7499 (mp0) cc_final: 0.6999 (tp30) REVERT: A 696 LYS cc_start: 0.7227 (tttp) cc_final: 0.6890 (ttpt) REVERT: B 36 ASN cc_start: 0.5452 (m-40) cc_final: 0.5208 (m110) REVERT: B 56 THR cc_start: 0.5646 (p) cc_final: 0.4937 (m) REVERT: B 57 VAL cc_start: 0.5403 (t) cc_final: 0.5070 (p) REVERT: B 82 ILE cc_start: 0.5059 (pt) cc_final: 0.4773 (pp) REVERT: B 288 LYS cc_start: 0.6546 (ttpp) cc_final: 0.6308 (pttp) REVERT: B 322 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.5827 (mmt90) REVERT: B 378 LEU cc_start: 0.7372 (tm) cc_final: 0.7055 (tp) REVERT: B 401 ASN cc_start: 0.6071 (m110) cc_final: 0.5593 (m-40) REVERT: B 402 GLU cc_start: 0.5937 (mp0) cc_final: 0.5560 (tp30) REVERT: B 426 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.5791 (mtmt) REVERT: B 460 ASN cc_start: 0.5361 (OUTLIER) cc_final: 0.5059 (p0) REVERT: B 478 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: B 546 GLU cc_start: 0.7982 (tt0) cc_final: 0.7520 (mt-10) REVERT: B 561 GLU cc_start: 0.7527 (mp0) cc_final: 0.7019 (tp30) REVERT: B 624 ASN cc_start: 0.7755 (p0) cc_final: 0.7549 (m-40) REVERT: B 693 ARG cc_start: 0.7083 (ttt90) cc_final: 0.6880 (ttt90) REVERT: B 696 LYS cc_start: 0.7297 (tttp) cc_final: 0.7021 (ttpt) REVERT: C 36 ASN cc_start: 0.5384 (m-40) cc_final: 0.5078 (m110) REVERT: C 56 THR cc_start: 0.5683 (p) cc_final: 0.4953 (m) REVERT: C 60 LYS cc_start: 0.4765 (mmtm) cc_final: 0.4390 (mppt) REVERT: C 82 ILE cc_start: 0.5081 (OUTLIER) cc_final: 0.4773 (pp) REVERT: C 101 SER cc_start: 0.4643 (t) cc_final: 0.4351 (m) REVERT: C 110 TYR cc_start: 0.3790 (m-10) cc_final: 0.3541 (m-10) REVERT: C 294 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5583 (tt0) REVERT: C 322 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5758 (mmt90) REVERT: C 401 ASN cc_start: 0.6022 (m110) cc_final: 0.5593 (m110) REVERT: C 426 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5838 (mtmt) REVERT: C 478 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: C 491 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6728 (mt-10) REVERT: C 505 LYS cc_start: 0.5987 (mtpt) cc_final: 0.5762 (tppp) REVERT: C 546 GLU cc_start: 0.8018 (tt0) cc_final: 0.7506 (mt-10) REVERT: C 561 GLU cc_start: 0.7365 (mp0) cc_final: 0.6849 (tp30) REVERT: C 696 LYS cc_start: 0.7340 (tttp) cc_final: 0.6985 (ttpt) REVERT: C 732 ARG cc_start: 0.4852 (mtm-85) cc_final: 0.4629 (mtm180) REVERT: D 36 ASN cc_start: 0.5459 (m-40) cc_final: 0.5230 (m110) REVERT: D 56 THR cc_start: 0.5796 (p) cc_final: 0.4953 (m) REVERT: D 57 VAL cc_start: 0.5166 (t) cc_final: 0.4823 (p) REVERT: D 82 ILE cc_start: 0.5120 (OUTLIER) cc_final: 0.4795 (pp) REVERT: D 110 TYR cc_start: 0.3680 (m-10) cc_final: 0.3205 (m-10) REVERT: D 291 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5422 (tm-30) REVERT: D 322 ARG cc_start: 0.6514 (mtt90) cc_final: 0.6259 (mpt-90) REVERT: D 378 LEU cc_start: 0.7385 (tm) cc_final: 0.6984 (tp) REVERT: D 379 GLU cc_start: 0.6959 (mp0) cc_final: 0.6752 (mp0) REVERT: D 401 ASN cc_start: 0.6143 (m110) cc_final: 0.5700 (m-40) REVERT: D 402 GLU cc_start: 0.6069 (mp0) cc_final: 0.5808 (tp30) REVERT: D 449 MET cc_start: 0.6898 (tpt) cc_final: 0.6490 (tpt) REVERT: D 460 ASN cc_start: 0.5271 (OUTLIER) cc_final: 0.4875 (p0) REVERT: D 473 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6385 (mm110) REVERT: D 478 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: D 491 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6605 (mt-10) REVERT: D 505 LYS cc_start: 0.5965 (mtpt) cc_final: 0.5656 (tppp) REVERT: D 546 GLU cc_start: 0.7921 (tt0) cc_final: 0.7472 (mt-10) REVERT: D 696 LYS cc_start: 0.7228 (tttp) cc_final: 0.6897 (ttpt) REVERT: E 36 ASN cc_start: 0.5457 (m-40) cc_final: 0.5210 (m110) REVERT: E 56 THR cc_start: 0.5610 (p) cc_final: 0.4904 (m) REVERT: E 57 VAL cc_start: 0.5420 (t) cc_final: 0.5111 (p) REVERT: E 60 LYS cc_start: 0.4936 (mmtm) cc_final: 0.4692 (mmtm) REVERT: E 82 ILE cc_start: 0.5009 (pt) cc_final: 0.4735 (pp) REVERT: E 110 TYR cc_start: 0.3760 (m-10) cc_final: 0.3510 (m-10) REVERT: E 288 LYS cc_start: 0.6529 (ttpp) cc_final: 0.6301 (pttp) REVERT: E 322 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.5818 (mmt90) REVERT: E 378 LEU cc_start: 0.7359 (tm) cc_final: 0.7047 (tp) REVERT: E 401 ASN cc_start: 0.6047 (m110) cc_final: 0.5550 (m-40) REVERT: E 402 GLU cc_start: 0.6028 (mp0) cc_final: 0.5617 (tp30) REVERT: E 426 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.5854 (mtmt) REVERT: E 460 ASN cc_start: 0.5352 (OUTLIER) cc_final: 0.5048 (p0) REVERT: E 478 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: E 546 GLU cc_start: 0.7985 (tt0) cc_final: 0.7524 (mt-10) REVERT: E 561 GLU cc_start: 0.7556 (mp0) cc_final: 0.7031 (tp30) REVERT: E 624 ASN cc_start: 0.7786 (p0) cc_final: 0.7557 (m110) REVERT: E 696 LYS cc_start: 0.7297 (tttp) cc_final: 0.7020 (ttpt) REVERT: E 758 PHE cc_start: 0.6106 (t80) cc_final: 0.5898 (t80) REVERT: F 36 ASN cc_start: 0.5381 (m-40) cc_final: 0.5077 (m110) REVERT: F 56 THR cc_start: 0.5682 (p) cc_final: 0.4952 (m) REVERT: F 60 LYS cc_start: 0.4764 (mmtm) cc_final: 0.4391 (mppt) REVERT: F 82 ILE cc_start: 0.5081 (OUTLIER) cc_final: 0.4773 (pp) REVERT: F 101 SER cc_start: 0.4639 (t) cc_final: 0.4348 (m) REVERT: F 110 TYR cc_start: 0.3790 (m-10) cc_final: 0.3543 (m-10) REVERT: F 294 GLU cc_start: 0.5791 (OUTLIER) cc_final: 0.5578 (tt0) REVERT: F 322 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5777 (mmt90) REVERT: F 401 ASN cc_start: 0.6033 (m110) cc_final: 0.5595 (m110) REVERT: F 402 GLU cc_start: 0.5897 (mp0) cc_final: 0.5691 (tp30) REVERT: F 426 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.5841 (mtmt) REVERT: F 478 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: F 505 LYS cc_start: 0.5990 (mtpt) cc_final: 0.5764 (tppp) REVERT: F 546 GLU cc_start: 0.8016 (tt0) cc_final: 0.7506 (mt-10) REVERT: F 561 GLU cc_start: 0.7371 (mp0) cc_final: 0.6850 (tp30) REVERT: F 696 LYS cc_start: 0.7333 (tttp) cc_final: 0.6983 (ttpt) REVERT: F 732 ARG cc_start: 0.4852 (mtm-85) cc_final: 0.4632 (mtm180) outliers start: 154 outliers final: 74 residues processed: 669 average time/residue: 1.5968 time to fit residues: 1254.3328 Evaluate side-chains 593 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 489 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 69 CYS Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 294 GLU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 203 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 394 optimal weight: 9.9990 chunk 417 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 373 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 536 GLN C 558 ASN C 568 GLN C 624 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN F 317 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN F 536 GLN F 558 ASN F 568 GLN F 624 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34854 Z= 0.273 Angle : 0.741 9.284 47142 Z= 0.367 Chirality : 0.047 0.170 5316 Planarity : 0.005 0.038 6186 Dihedral : 8.213 91.634 4836 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.07 % Rotamer: Outliers : 5.20 % Allowed : 17.99 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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: -2.20 (0.12), residues: 4314 helix: -1.05 (0.12), residues: 1680 sheet: -0.62 (0.21), residues: 570 loop : -2.03 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 551 HIS 0.005 0.002 HIS E 735 PHE 0.014 0.002 PHE E 139 TYR 0.014 0.002 TYR E 644 ARG 0.005 0.001 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 533 time to evaluate : 4.030 Fit side-chains revert: symmetry clash REVERT: A 36 ASN cc_start: 0.5459 (m-40) cc_final: 0.5233 (m110) REVERT: A 53 ARG cc_start: 0.3881 (ttm110) cc_final: 0.3555 (ptp90) REVERT: A 56 THR cc_start: 0.5737 (p) cc_final: 0.4940 (m) REVERT: A 82 ILE cc_start: 0.5123 (OUTLIER) cc_final: 0.4837 (pp) REVERT: A 150 ASP cc_start: 0.4057 (m-30) cc_final: 0.3551 (p0) REVERT: A 291 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5415 (tm-30) REVERT: A 322 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5758 (mmt90) REVERT: A 379 GLU cc_start: 0.6958 (mp0) cc_final: 0.6665 (mp0) REVERT: A 401 ASN cc_start: 0.6144 (m110) cc_final: 0.5691 (m-40) REVERT: A 402 GLU cc_start: 0.6078 (mp0) cc_final: 0.5748 (tp30) REVERT: A 449 MET cc_start: 0.6788 (tpt) cc_final: 0.6538 (tpp) REVERT: A 453 ARG cc_start: 0.6371 (mtm110) cc_final: 0.5797 (ttm-80) REVERT: A 460 ASN cc_start: 0.5279 (OUTLIER) cc_final: 0.4880 (p0) REVERT: A 473 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6353 (mm110) REVERT: A 478 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: A 491 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6673 (mt-10) REVERT: A 505 LYS cc_start: 0.5996 (mtpt) cc_final: 0.5663 (tppp) REVERT: A 546 GLU cc_start: 0.7906 (tt0) cc_final: 0.7568 (mt-10) REVERT: A 561 GLU cc_start: 0.7496 (mp0) cc_final: 0.7003 (tp30) REVERT: A 614 LYS cc_start: 0.5751 (mtmm) cc_final: 0.5153 (mptp) REVERT: A 696 LYS cc_start: 0.7240 (tttp) cc_final: 0.6903 (ttpt) REVERT: B 36 ASN cc_start: 0.5550 (m-40) cc_final: 0.5316 (m110) REVERT: B 56 THR cc_start: 0.5584 (p) cc_final: 0.4932 (m) REVERT: B 57 VAL cc_start: 0.5356 (t) cc_final: 0.5030 (p) REVERT: B 82 ILE cc_start: 0.5046 (OUTLIER) cc_final: 0.4807 (pp) REVERT: B 154 VAL cc_start: 0.5540 (OUTLIER) cc_final: 0.5338 (t) REVERT: B 288 LYS cc_start: 0.6483 (ttpp) cc_final: 0.6274 (pttp) REVERT: B 322 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.5809 (mmt90) REVERT: B 366 GLU cc_start: 0.7283 (tt0) cc_final: 0.7074 (tp30) REVERT: B 377 ARG cc_start: 0.7348 (mtm-85) cc_final: 0.7132 (mtm180) REVERT: B 378 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7038 (tp) REVERT: B 401 ASN cc_start: 0.6074 (m110) cc_final: 0.5624 (m-40) REVERT: B 402 GLU cc_start: 0.5970 (mp0) cc_final: 0.5614 (tp30) REVERT: B 460 ASN cc_start: 0.5300 (OUTLIER) cc_final: 0.4993 (p0) REVERT: B 478 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: B 546 GLU cc_start: 0.7991 (tt0) cc_final: 0.7513 (mt-10) REVERT: B 561 GLU cc_start: 0.7507 (mp0) cc_final: 0.7006 (tp30) REVERT: B 614 LYS cc_start: 0.5553 (mtmm) cc_final: 0.5029 (mptp) REVERT: B 624 ASN cc_start: 0.7802 (p0) cc_final: 0.7579 (m-40) REVERT: B 696 LYS cc_start: 0.7272 (tttp) cc_final: 0.6972 (ttpt) REVERT: C 36 ASN cc_start: 0.5432 (m-40) cc_final: 0.5160 (m110) REVERT: C 51 LEU cc_start: 0.2471 (OUTLIER) cc_final: 0.2037 (tp) REVERT: C 56 THR cc_start: 0.5658 (p) cc_final: 0.4940 (m) REVERT: C 60 LYS cc_start: 0.4751 (mmtm) cc_final: 0.4543 (mmtm) REVERT: C 82 ILE cc_start: 0.5080 (OUTLIER) cc_final: 0.4831 (pp) REVERT: C 150 ASP cc_start: 0.4221 (m-30) cc_final: 0.3653 (p0) REVERT: C 165 VAL cc_start: 0.4142 (OUTLIER) cc_final: 0.3685 (p) REVERT: C 316 THR cc_start: 0.4640 (t) cc_final: 0.4435 (p) REVERT: C 322 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.5907 (mtt90) REVERT: C 401 ASN cc_start: 0.6101 (m110) cc_final: 0.5737 (m110) REVERT: C 453 ARG cc_start: 0.5787 (mtm180) cc_final: 0.5427 (ptp-170) REVERT: C 478 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: C 491 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6718 (mt-10) REVERT: C 505 LYS cc_start: 0.6064 (mtpt) cc_final: 0.5806 (tppp) REVERT: C 546 GLU cc_start: 0.8002 (tt0) cc_final: 0.7542 (mt-10) REVERT: C 561 GLU cc_start: 0.7339 (mp0) cc_final: 0.6852 (tp30) REVERT: C 696 LYS cc_start: 0.7274 (tttp) cc_final: 0.6982 (ttpt) REVERT: C 732 ARG cc_start: 0.4876 (mtm-85) cc_final: 0.4659 (mtm180) REVERT: D 36 ASN cc_start: 0.5484 (m-40) cc_final: 0.5267 (m110) REVERT: D 51 LEU cc_start: 0.2430 (OUTLIER) cc_final: 0.2107 (tp) REVERT: D 56 THR cc_start: 0.5819 (p) cc_final: 0.5010 (m) REVERT: D 82 ILE cc_start: 0.5119 (OUTLIER) cc_final: 0.4830 (pp) REVERT: D 150 ASP cc_start: 0.4059 (m-30) cc_final: 0.3552 (p0) REVERT: D 291 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5402 (tm-30) REVERT: D 322 ARG cc_start: 0.6463 (mtt90) cc_final: 0.6214 (mpt-90) REVERT: D 379 GLU cc_start: 0.6960 (mp0) cc_final: 0.6667 (mp0) REVERT: D 401 ASN cc_start: 0.6146 (m110) cc_final: 0.5711 (m-40) REVERT: D 402 GLU cc_start: 0.6080 (mp0) cc_final: 0.5751 (tp30) REVERT: D 449 MET cc_start: 0.6872 (tpt) cc_final: 0.6593 (tpt) REVERT: D 460 ASN cc_start: 0.5272 (OUTLIER) cc_final: 0.4844 (p0) REVERT: D 473 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6353 (mm110) REVERT: D 478 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6966 (m-30) REVERT: D 491 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6604 (mt-10) REVERT: D 505 LYS cc_start: 0.6017 (mtpt) cc_final: 0.5677 (tppp) REVERT: D 546 GLU cc_start: 0.7905 (tt0) cc_final: 0.7568 (mt-10) REVERT: D 561 GLU cc_start: 0.7472 (mp0) cc_final: 0.6990 (tp30) REVERT: D 614 LYS cc_start: 0.5220 (mppt) cc_final: 0.4836 (mptp) REVERT: D 696 LYS cc_start: 0.7241 (tttp) cc_final: 0.6908 (ttpt) REVERT: E 36 ASN cc_start: 0.5560 (m-40) cc_final: 0.5325 (m110) REVERT: E 56 THR cc_start: 0.5549 (p) cc_final: 0.4894 (m) REVERT: E 82 ILE cc_start: 0.5036 (OUTLIER) cc_final: 0.4790 (pp) REVERT: E 110 TYR cc_start: 0.3780 (m-10) cc_final: 0.3570 (m-10) REVERT: E 154 VAL cc_start: 0.5541 (OUTLIER) cc_final: 0.5337 (t) REVERT: E 288 LYS cc_start: 0.6510 (ttpp) cc_final: 0.6306 (pttp) REVERT: E 322 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.5777 (mmt90) REVERT: E 366 GLU cc_start: 0.7283 (tt0) cc_final: 0.7074 (tp30) REVERT: E 377 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.7146 (mtm180) REVERT: E 378 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7040 (tp) REVERT: E 401 ASN cc_start: 0.6071 (m110) cc_final: 0.5625 (m-40) REVERT: E 402 GLU cc_start: 0.5995 (mp0) cc_final: 0.5658 (tp30) REVERT: E 449 MET cc_start: 0.6852 (tpt) cc_final: 0.6625 (tpp) REVERT: E 453 ARG cc_start: 0.5738 (mtm180) cc_final: 0.5412 (ttm-80) REVERT: E 460 ASN cc_start: 0.5363 (OUTLIER) cc_final: 0.5056 (p0) REVERT: E 478 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: E 546 GLU cc_start: 0.7991 (tt0) cc_final: 0.7514 (mt-10) REVERT: E 561 GLU cc_start: 0.7548 (mp0) cc_final: 0.7042 (tp30) REVERT: E 614 LYS cc_start: 0.5598 (mtmm) cc_final: 0.5047 (mptp) REVERT: E 662 ARG cc_start: 0.4934 (ttp-110) cc_final: 0.4646 (ptt90) REVERT: E 696 LYS cc_start: 0.7291 (tttp) cc_final: 0.6962 (ttpt) REVERT: F 36 ASN cc_start: 0.5474 (m-40) cc_final: 0.5197 (m110) REVERT: F 51 LEU cc_start: 0.2472 (OUTLIER) cc_final: 0.2038 (tp) REVERT: F 56 THR cc_start: 0.5663 (p) cc_final: 0.4943 (m) REVERT: F 60 LYS cc_start: 0.4751 (mmtm) cc_final: 0.4545 (mmtm) REVERT: F 82 ILE cc_start: 0.5081 (OUTLIER) cc_final: 0.4830 (pp) REVERT: F 150 ASP cc_start: 0.4218 (m-30) cc_final: 0.3652 (p0) REVERT: F 165 VAL cc_start: 0.4143 (OUTLIER) cc_final: 0.3685 (p) REVERT: F 239 ARG cc_start: 0.5994 (mmm-85) cc_final: 0.5629 (mmm160) REVERT: F 322 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6011 (mtt90) REVERT: F 401 ASN cc_start: 0.6021 (m110) cc_final: 0.5560 (m110) REVERT: F 402 GLU cc_start: 0.5941 (mp0) cc_final: 0.5674 (tp30) REVERT: F 453 ARG cc_start: 0.5776 (mtm180) cc_final: 0.5412 (ptp-170) REVERT: F 478 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: F 505 LYS cc_start: 0.6050 (mtpt) cc_final: 0.5796 (tppp) REVERT: F 546 GLU cc_start: 0.8003 (tt0) cc_final: 0.7542 (mt-10) REVERT: F 561 GLU cc_start: 0.7335 (mp0) cc_final: 0.6849 (tp30) REVERT: F 696 LYS cc_start: 0.7272 (tttp) cc_final: 0.6981 (ttpt) REVERT: F 732 ARG cc_start: 0.4875 (mtm-85) cc_final: 0.4661 (mtm180) outliers start: 192 outliers final: 70 residues processed: 683 average time/residue: 1.4753 time to fit residues: 1195.6777 Evaluate side-chains 597 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 493 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 749 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 20.0000 chunk 237 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 356 optimal weight: 10.0000 chunk 288 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 374 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN B 36 ASN B 85 ASN B 296 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN E 36 ASN E 85 ASN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34854 Z= 0.332 Angle : 0.801 10.336 47142 Z= 0.399 Chirality : 0.050 0.300 5316 Planarity : 0.006 0.046 6186 Dihedral : 8.550 97.437 4836 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.02 % Favored : 91.84 % Rotamer: Outliers : 6.80 % Allowed : 18.13 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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: -2.31 (0.12), residues: 4314 helix: -1.12 (0.11), residues: 1686 sheet: -0.73 (0.21), residues: 600 loop : -2.11 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 551 HIS 0.007 0.002 HIS B 735 PHE 0.016 0.002 PHE D 139 TYR 0.013 0.002 TYR B 755 ARG 0.007 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 527 time to evaluate : 3.814 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.5770 (p) cc_final: 0.4937 (m) REVERT: A 82 ILE cc_start: 0.5155 (OUTLIER) cc_final: 0.4799 (pp) REVERT: A 141 GLU cc_start: 0.2184 (OUTLIER) cc_final: 0.1942 (pt0) REVERT: A 150 ASP cc_start: 0.4061 (m-30) cc_final: 0.3512 (p0) REVERT: A 291 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5552 (tm-30) REVERT: A 322 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.5864 (mmt90) REVERT: A 379 GLU cc_start: 0.6861 (mp0) cc_final: 0.6548 (mp0) REVERT: A 401 ASN cc_start: 0.6106 (m110) cc_final: 0.5629 (m-40) REVERT: A 402 GLU cc_start: 0.6021 (mp0) cc_final: 0.5607 (tp30) REVERT: A 426 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.5680 (mtmt) REVERT: A 449 MET cc_start: 0.6802 (tpt) cc_final: 0.6584 (tpp) REVERT: A 453 ARG cc_start: 0.6328 (mtm110) cc_final: 0.5674 (ttm-80) REVERT: A 460 ASN cc_start: 0.5380 (OUTLIER) cc_final: 0.4997 (p0) REVERT: A 473 GLN cc_start: 0.6631 (OUTLIER) cc_final: 0.6340 (mm110) REVERT: A 505 LYS cc_start: 0.6003 (mtpt) cc_final: 0.5633 (tppp) REVERT: A 546 GLU cc_start: 0.7919 (tt0) cc_final: 0.7475 (mt-10) REVERT: A 614 LYS cc_start: 0.5867 (mtmm) cc_final: 0.5229 (mptp) REVERT: A 662 ARG cc_start: 0.5056 (ttm110) cc_final: 0.4554 (mtm110) REVERT: A 696 LYS cc_start: 0.7200 (tttp) cc_final: 0.6893 (ttpt) REVERT: B 56 THR cc_start: 0.5664 (p) cc_final: 0.4928 (m) REVERT: B 82 ILE cc_start: 0.5033 (OUTLIER) cc_final: 0.4736 (pp) REVERT: B 85 ASN cc_start: 0.6454 (OUTLIER) cc_final: 0.5661 (m110) REVERT: B 110 TYR cc_start: 0.3923 (m-10) cc_final: 0.3170 (m-10) REVERT: B 288 LYS cc_start: 0.6509 (ttpp) cc_final: 0.6305 (pttp) REVERT: B 322 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.5823 (mmt90) REVERT: B 366 GLU cc_start: 0.7311 (tt0) cc_final: 0.7078 (tp30) REVERT: B 377 ARG cc_start: 0.7388 (mtm-85) cc_final: 0.7110 (mtm180) REVERT: B 378 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7063 (tp) REVERT: B 401 ASN cc_start: 0.6138 (m110) cc_final: 0.5640 (m-40) REVERT: B 402 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5618 (tp30) REVERT: B 426 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.5692 (mtmt) REVERT: B 453 ARG cc_start: 0.5882 (mtm180) cc_final: 0.5555 (ttm-80) REVERT: B 546 GLU cc_start: 0.7964 (tt0) cc_final: 0.7450 (mt-10) REVERT: B 554 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: B 561 GLU cc_start: 0.7522 (mp0) cc_final: 0.7024 (tp30) REVERT: B 614 LYS cc_start: 0.5603 (OUTLIER) cc_final: 0.5053 (mptp) REVERT: B 624 ASN cc_start: 0.7818 (p0) cc_final: 0.7513 (m-40) REVERT: B 691 CYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6708 (m) REVERT: B 696 LYS cc_start: 0.7314 (tttp) cc_final: 0.7017 (ttpt) REVERT: C 56 THR cc_start: 0.5689 (p) cc_final: 0.4934 (m) REVERT: C 60 LYS cc_start: 0.4887 (mmtm) cc_final: 0.4632 (mmtm) REVERT: C 82 ILE cc_start: 0.5081 (OUTLIER) cc_final: 0.4748 (pp) REVERT: C 120 ASP cc_start: 0.0421 (OUTLIER) cc_final: -0.0197 (t0) REVERT: C 322 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5742 (mmt90) REVERT: C 377 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.7092 (mtm180) REVERT: C 401 ASN cc_start: 0.6099 (m110) cc_final: 0.5665 (m110) REVERT: C 426 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5628 (mtmt) REVERT: C 505 LYS cc_start: 0.5990 (mtpt) cc_final: 0.5773 (tppp) REVERT: C 546 GLU cc_start: 0.8012 (tt0) cc_final: 0.7540 (mt-10) REVERT: C 561 GLU cc_start: 0.7355 (mp0) cc_final: 0.6879 (tp30) REVERT: C 696 LYS cc_start: 0.7272 (tttp) cc_final: 0.6979 (ttpt) REVERT: C 732 ARG cc_start: 0.4805 (mtm-85) cc_final: 0.4586 (mtm180) REVERT: C 738 GLU cc_start: 0.5758 (tp30) cc_final: 0.5526 (tp30) REVERT: D 56 THR cc_start: 0.5850 (p) cc_final: 0.4977 (m) REVERT: D 82 ILE cc_start: 0.5186 (OUTLIER) cc_final: 0.4836 (pp) REVERT: D 141 GLU cc_start: 0.2194 (OUTLIER) cc_final: 0.1959 (pt0) REVERT: D 150 ASP cc_start: 0.4072 (m-30) cc_final: 0.3530 (p0) REVERT: D 291 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5825 (tt0) REVERT: D 322 ARG cc_start: 0.6431 (mtt90) cc_final: 0.6083 (mpt-90) REVERT: D 379 GLU cc_start: 0.6860 (mp0) cc_final: 0.6547 (mp0) REVERT: D 401 ASN cc_start: 0.6109 (m110) cc_final: 0.5613 (m-40) REVERT: D 402 GLU cc_start: 0.6022 (mp0) cc_final: 0.5622 (tp30) REVERT: D 449 MET cc_start: 0.6759 (tpt) cc_final: 0.6496 (tpt) REVERT: D 453 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5592 (ptp-170) REVERT: D 460 ASN cc_start: 0.5396 (OUTLIER) cc_final: 0.4959 (p0) REVERT: D 473 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6342 (mm110) REVERT: D 478 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: D 505 LYS cc_start: 0.5994 (mtpt) cc_final: 0.5624 (tppp) REVERT: D 546 GLU cc_start: 0.7917 (tt0) cc_final: 0.7473 (mt-10) REVERT: D 662 ARG cc_start: 0.5877 (mtp-110) cc_final: 0.5068 (mtm110) REVERT: D 696 LYS cc_start: 0.7235 (tttp) cc_final: 0.6927 (ttpt) REVERT: E 56 THR cc_start: 0.5578 (p) cc_final: 0.4838 (m) REVERT: E 60 LYS cc_start: 0.5124 (mmtm) cc_final: 0.4694 (mmtm) REVERT: E 82 ILE cc_start: 0.5073 (OUTLIER) cc_final: 0.4771 (pp) REVERT: E 85 ASN cc_start: 0.6465 (OUTLIER) cc_final: 0.5714 (m110) REVERT: E 288 LYS cc_start: 0.6498 (ttpp) cc_final: 0.6294 (pttp) REVERT: E 322 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.5813 (mmt90) REVERT: E 366 GLU cc_start: 0.7311 (tt0) cc_final: 0.7076 (tp30) REVERT: E 377 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7122 (mtm180) REVERT: E 378 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7052 (tp) REVERT: E 401 ASN cc_start: 0.6107 (m110) cc_final: 0.5629 (m-40) REVERT: E 402 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5590 (tp30) REVERT: E 426 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.5754 (mtmt) REVERT: E 449 MET cc_start: 0.6846 (tpt) cc_final: 0.6614 (tpp) REVERT: E 453 ARG cc_start: 0.5880 (mtm180) cc_final: 0.5503 (ttm-80) REVERT: E 460 ASN cc_start: 0.5461 (OUTLIER) cc_final: 0.5133 (p0) REVERT: E 546 GLU cc_start: 0.7965 (tt0) cc_final: 0.7452 (mt-10) REVERT: E 561 GLU cc_start: 0.7540 (mp0) cc_final: 0.7040 (tp30) REVERT: E 614 LYS cc_start: 0.5742 (mtmm) cc_final: 0.5174 (mptp) REVERT: E 691 CYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6700 (m) REVERT: E 696 LYS cc_start: 0.7305 (tttp) cc_final: 0.6947 (ttpt) REVERT: F 56 THR cc_start: 0.5688 (p) cc_final: 0.4934 (m) REVERT: F 60 LYS cc_start: 0.4886 (mmtm) cc_final: 0.4632 (mmtm) REVERT: F 82 ILE cc_start: 0.5066 (OUTLIER) cc_final: 0.4739 (pp) REVERT: F 120 ASP cc_start: 0.0422 (OUTLIER) cc_final: -0.0195 (t0) REVERT: F 322 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5743 (mmt90) REVERT: F 377 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7001 (mtm180) REVERT: F 401 ASN cc_start: 0.5982 (m110) cc_final: 0.5535 (m110) REVERT: F 402 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5591 (tp30) REVERT: F 426 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5620 (mtmt) REVERT: F 453 ARG cc_start: 0.5870 (mtm180) cc_final: 0.5487 (ptp-170) REVERT: F 505 LYS cc_start: 0.5998 (mtpt) cc_final: 0.5769 (tppp) REVERT: F 546 GLU cc_start: 0.8012 (tt0) cc_final: 0.7538 (mt-10) REVERT: F 561 GLU cc_start: 0.7350 (mp0) cc_final: 0.6858 (tp30) REVERT: F 696 LYS cc_start: 0.7273 (tttp) cc_final: 0.6981 (ttpt) REVERT: F 732 ARG cc_start: 0.4801 (mtm-85) cc_final: 0.4585 (mtm180) outliers start: 251 outliers final: 112 residues processed: 732 average time/residue: 1.4951 time to fit residues: 1297.7918 Evaluate side-chains 642 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 490 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 691 CYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 649 ASP Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 8.9990 chunk 376 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 245 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 417 optimal weight: 20.0000 chunk 346 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN A 616 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN C 750 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN D 616 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN F 750 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 34854 Z= 0.319 Angle : 0.790 9.872 47142 Z= 0.393 Chirality : 0.049 0.237 5316 Planarity : 0.006 0.063 6186 Dihedral : 8.464 95.348 4836 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.23 % Favored : 91.63 % Rotamer: Outliers : 6.42 % Allowed : 19.70 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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: -2.22 (0.12), residues: 4314 helix: -1.02 (0.12), residues: 1686 sheet: -0.59 (0.21), residues: 588 loop : -2.12 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 551 HIS 0.005 0.002 HIS B 735 PHE 0.014 0.002 PHE C 139 TYR 0.014 0.002 TYR E 644 ARG 0.006 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 502 time to evaluate : 3.855 Fit side-chains REVERT: A 56 THR cc_start: 0.5838 (p) cc_final: 0.4977 (m) REVERT: A 82 ILE cc_start: 0.5106 (OUTLIER) cc_final: 0.4751 (pp) REVERT: A 141 GLU cc_start: 0.2212 (OUTLIER) cc_final: 0.1983 (pt0) REVERT: A 150 ASP cc_start: 0.4059 (m-30) cc_final: 0.3495 (p0) REVERT: A 151 ILE cc_start: 0.5851 (OUTLIER) cc_final: 0.5149 (mp) REVERT: A 291 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5586 (tm-30) REVERT: A 322 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.5822 (mmt90) REVERT: A 379 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: A 388 MET cc_start: 0.5876 (mtt) cc_final: 0.5641 (mtt) REVERT: A 401 ASN cc_start: 0.6156 (m110) cc_final: 0.5677 (m-40) REVERT: A 402 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5582 (tp30) REVERT: A 426 LYS cc_start: 0.6487 (OUTLIER) cc_final: 0.5693 (mtmt) REVERT: A 442 MET cc_start: 0.5461 (OUTLIER) cc_final: 0.5214 (ttp) REVERT: A 449 MET cc_start: 0.6784 (tpt) cc_final: 0.6545 (tpp) REVERT: A 453 ARG cc_start: 0.6330 (mtm110) cc_final: 0.5669 (ttm-80) REVERT: A 460 ASN cc_start: 0.5377 (OUTLIER) cc_final: 0.4941 (p0) REVERT: A 473 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6356 (mm110) REVERT: A 505 LYS cc_start: 0.5964 (mtpt) cc_final: 0.5547 (tppp) REVERT: A 546 GLU cc_start: 0.7918 (tt0) cc_final: 0.7472 (mt-10) REVERT: A 614 LYS cc_start: 0.5855 (mtmm) cc_final: 0.5252 (mptp) REVERT: A 662 ARG cc_start: 0.5209 (ttm110) cc_final: 0.4764 (mtm110) REVERT: A 696 LYS cc_start: 0.7171 (tttp) cc_final: 0.6817 (ttpt) REVERT: B 56 THR cc_start: 0.5677 (p) cc_final: 0.4936 (m) REVERT: B 82 ILE cc_start: 0.4991 (OUTLIER) cc_final: 0.4719 (pp) REVERT: B 110 TYR cc_start: 0.3938 (m-10) cc_final: 0.3194 (m-10) REVERT: B 126 ILE cc_start: 0.3743 (OUTLIER) cc_final: 0.3451 (tt) REVERT: B 154 VAL cc_start: 0.5624 (t) cc_final: 0.5419 (t) REVERT: B 210 ARG cc_start: 0.5782 (ttp-110) cc_final: 0.5459 (tpt90) REVERT: B 288 LYS cc_start: 0.6507 (ttpp) cc_final: 0.6295 (pttp) REVERT: B 322 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.5838 (mmt90) REVERT: B 366 GLU cc_start: 0.7319 (tt0) cc_final: 0.7111 (tp30) REVERT: B 377 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7151 (mtm180) REVERT: B 378 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7057 (tp) REVERT: B 401 ASN cc_start: 0.6124 (m110) cc_final: 0.5646 (m-40) REVERT: B 402 GLU cc_start: 0.5980 (OUTLIER) cc_final: 0.5576 (tp30) REVERT: B 426 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5639 (mtmt) REVERT: B 453 ARG cc_start: 0.5918 (mtm180) cc_final: 0.5511 (ttm-80) REVERT: B 546 GLU cc_start: 0.7971 (tt0) cc_final: 0.7506 (mt-10) REVERT: B 554 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: B 614 LYS cc_start: 0.5530 (mtmm) cc_final: 0.5055 (mptp) REVERT: B 624 ASN cc_start: 0.7849 (p0) cc_final: 0.7630 (p0) REVERT: B 662 ARG cc_start: 0.5079 (ttm110) cc_final: 0.4623 (mtm110) REVERT: B 691 CYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6684 (m) REVERT: B 696 LYS cc_start: 0.7306 (tttp) cc_final: 0.6986 (ttpt) REVERT: C 56 THR cc_start: 0.5663 (p) cc_final: 0.4940 (m) REVERT: C 60 LYS cc_start: 0.4873 (mmtm) cc_final: 0.4579 (mmtm) REVERT: C 82 ILE cc_start: 0.5074 (OUTLIER) cc_final: 0.4780 (pp) REVERT: C 110 TYR cc_start: 0.3686 (m-10) cc_final: 0.3296 (m-10) REVERT: C 120 ASP cc_start: 0.0307 (OUTLIER) cc_final: -0.0324 (t0) REVERT: C 150 ASP cc_start: 0.4168 (m-30) cc_final: 0.3639 (p0) REVERT: C 322 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5681 (mmt90) REVERT: C 377 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.7056 (mtm180) REVERT: C 401 ASN cc_start: 0.6132 (m110) cc_final: 0.5690 (m110) REVERT: C 426 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.5568 (mtmt) REVERT: C 453 ARG cc_start: 0.5908 (mtm180) cc_final: 0.5537 (ptp-170) REVERT: C 470 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7069 (pp20) REVERT: C 478 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7007 (m-30) REVERT: C 505 LYS cc_start: 0.5990 (mtpt) cc_final: 0.5749 (tppp) REVERT: C 546 GLU cc_start: 0.8013 (tt0) cc_final: 0.7493 (mt-10) REVERT: C 561 GLU cc_start: 0.7355 (mp0) cc_final: 0.6881 (tp30) REVERT: C 662 ARG cc_start: 0.5892 (mtp-110) cc_final: 0.5116 (mtm110) REVERT: C 696 LYS cc_start: 0.7265 (tttp) cc_final: 0.6944 (ttpt) REVERT: D 56 THR cc_start: 0.5836 (p) cc_final: 0.4976 (m) REVERT: D 82 ILE cc_start: 0.5124 (OUTLIER) cc_final: 0.4772 (pp) REVERT: D 141 GLU cc_start: 0.2214 (OUTLIER) cc_final: 0.1989 (pt0) REVERT: D 150 ASP cc_start: 0.4064 (m-30) cc_final: 0.3499 (p0) REVERT: D 151 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5147 (mp) REVERT: D 379 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: D 401 ASN cc_start: 0.6125 (m110) cc_final: 0.5640 (m-40) REVERT: D 402 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5608 (tp30) REVERT: D 442 MET cc_start: 0.5460 (OUTLIER) cc_final: 0.5210 (ttp) REVERT: D 460 ASN cc_start: 0.5374 (OUTLIER) cc_final: 0.4959 (p0) REVERT: D 473 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6319 (mm110) REVERT: D 505 LYS cc_start: 0.5985 (mtpt) cc_final: 0.5567 (tppp) REVERT: D 546 GLU cc_start: 0.7927 (tt0) cc_final: 0.7483 (mt-10) REVERT: D 696 LYS cc_start: 0.7197 (tttp) cc_final: 0.6845 (ttpt) REVERT: E 56 THR cc_start: 0.5596 (p) cc_final: 0.4860 (m) REVERT: E 60 LYS cc_start: 0.5103 (mmtm) cc_final: 0.4699 (mmtm) REVERT: E 82 ILE cc_start: 0.5039 (OUTLIER) cc_final: 0.4760 (pp) REVERT: E 126 ILE cc_start: 0.3767 (OUTLIER) cc_final: 0.3467 (tt) REVERT: E 154 VAL cc_start: 0.5618 (t) cc_final: 0.5414 (t) REVERT: E 288 LYS cc_start: 0.6507 (ttpp) cc_final: 0.6287 (pttp) REVERT: E 322 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.5820 (mmt90) REVERT: E 366 GLU cc_start: 0.7318 (tt0) cc_final: 0.7106 (tp30) REVERT: E 377 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.7161 (mtm180) REVERT: E 378 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7069 (tp) REVERT: E 401 ASN cc_start: 0.6087 (m110) cc_final: 0.5627 (m-40) REVERT: E 402 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5529 (tp30) REVERT: E 426 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5749 (mtmt) REVERT: E 449 MET cc_start: 0.6852 (tpt) cc_final: 0.6615 (tpp) REVERT: E 453 ARG cc_start: 0.5900 (mtm180) cc_final: 0.5503 (ttm-80) REVERT: E 460 ASN cc_start: 0.5523 (OUTLIER) cc_final: 0.5206 (p0) REVERT: E 546 GLU cc_start: 0.7972 (tt0) cc_final: 0.7456 (mt-10) REVERT: E 554 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: E 561 GLU cc_start: 0.7537 (mp0) cc_final: 0.7040 (tp30) REVERT: E 614 LYS cc_start: 0.5780 (mtmm) cc_final: 0.5205 (mptp) REVERT: E 662 ARG cc_start: 0.5891 (mtp-110) cc_final: 0.5238 (mtm110) REVERT: E 691 CYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6682 (m) REVERT: E 696 LYS cc_start: 0.7321 (tttp) cc_final: 0.6976 (ttpt) REVERT: F 56 THR cc_start: 0.5660 (p) cc_final: 0.4939 (m) REVERT: F 60 LYS cc_start: 0.4872 (mmtm) cc_final: 0.4579 (mmtm) REVERT: F 82 ILE cc_start: 0.5069 (OUTLIER) cc_final: 0.4774 (pp) REVERT: F 110 TYR cc_start: 0.3680 (m-10) cc_final: 0.3292 (m-10) REVERT: F 120 ASP cc_start: 0.0308 (OUTLIER) cc_final: -0.0322 (t0) REVERT: F 322 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.5741 (mmt90) REVERT: F 401 ASN cc_start: 0.6034 (m110) cc_final: 0.5545 (m110) REVERT: F 402 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5588 (tp30) REVERT: F 426 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5567 (mtmt) REVERT: F 453 ARG cc_start: 0.5861 (mtm180) cc_final: 0.5486 (ptp-170) REVERT: F 470 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7076 (pp20) REVERT: F 478 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: F 505 LYS cc_start: 0.5950 (mtpt) cc_final: 0.5742 (tppp) REVERT: F 546 GLU cc_start: 0.8012 (tt0) cc_final: 0.7491 (mt-10) REVERT: F 561 GLU cc_start: 0.7355 (mp0) cc_final: 0.6869 (tp30) REVERT: F 662 ARG cc_start: 0.5891 (mtp-110) cc_final: 0.5109 (mtm110) REVERT: F 696 LYS cc_start: 0.7265 (tttp) cc_final: 0.6946 (ttpt) outliers start: 237 outliers final: 129 residues processed: 691 average time/residue: 1.5206 time to fit residues: 1245.0720 Evaluate side-chains 657 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 479 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 691 CYS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 649 ASP Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 416 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 253 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34854 Z= 0.326 Angle : 0.799 9.916 47142 Z= 0.397 Chirality : 0.049 0.231 5316 Planarity : 0.006 0.070 6186 Dihedral : 8.502 96.263 4836 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.32 % Favored : 91.54 % Rotamer: Outliers : 6.94 % Allowed : 20.03 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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: -2.29 (0.12), residues: 4314 helix: -0.99 (0.12), residues: 1674 sheet: -1.19 (0.19), residues: 696 loop : -2.05 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 551 HIS 0.006 0.002 HIS B 384 PHE 0.011 0.002 PHE D 267 TYR 0.014 0.002 TYR E 644 ARG 0.006 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 508 time to evaluate : 4.233 Fit side-chains REVERT: A 56 THR cc_start: 0.5739 (p) cc_final: 0.4895 (m) REVERT: A 82 ILE cc_start: 0.5107 (OUTLIER) cc_final: 0.4756 (pp) REVERT: A 141 GLU cc_start: 0.2285 (OUTLIER) cc_final: 0.1999 (pt0) REVERT: A 151 ILE cc_start: 0.5867 (OUTLIER) cc_final: 0.5413 (mp) REVERT: A 291 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5573 (tm-30) REVERT: A 322 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.5836 (mmt90) REVERT: A 378 LEU cc_start: 0.7416 (tm) cc_final: 0.6960 (tp) REVERT: A 379 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: A 401 ASN cc_start: 0.6116 (m110) cc_final: 0.5610 (m-40) REVERT: A 402 GLU cc_start: 0.6006 (OUTLIER) cc_final: 0.5532 (tp30) REVERT: A 426 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.5677 (mtmt) REVERT: A 442 MET cc_start: 0.5462 (OUTLIER) cc_final: 0.5261 (ttp) REVERT: A 449 MET cc_start: 0.6853 (tpt) cc_final: 0.6623 (tpp) REVERT: A 453 ARG cc_start: 0.6282 (mtm110) cc_final: 0.5599 (ttm-80) REVERT: A 460 ASN cc_start: 0.5434 (OUTLIER) cc_final: 0.5044 (p0) REVERT: A 505 LYS cc_start: 0.5894 (mtpt) cc_final: 0.5389 (tppp) REVERT: A 546 GLU cc_start: 0.7906 (tt0) cc_final: 0.7442 (mt-10) REVERT: A 614 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.5282 (mptp) REVERT: A 662 ARG cc_start: 0.5212 (ttm110) cc_final: 0.4981 (mtm110) REVERT: A 696 LYS cc_start: 0.7218 (tttp) cc_final: 0.6851 (ttpt) REVERT: A 750 ASN cc_start: 0.5135 (OUTLIER) cc_final: 0.4610 (t0) REVERT: B 82 ILE cc_start: 0.5070 (OUTLIER) cc_final: 0.4757 (pp) REVERT: B 110 TYR cc_start: 0.3882 (m-10) cc_final: 0.3143 (m-10) REVERT: B 126 ILE cc_start: 0.3733 (OUTLIER) cc_final: 0.3473 (tt) REVERT: B 154 VAL cc_start: 0.5621 (t) cc_final: 0.5412 (t) REVERT: B 210 ARG cc_start: 0.6053 (ttp-110) cc_final: 0.5495 (tpt90) REVERT: B 288 LYS cc_start: 0.6517 (ttpp) cc_final: 0.6282 (pttp) REVERT: B 322 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.5836 (mmt90) REVERT: B 366 GLU cc_start: 0.7314 (tt0) cc_final: 0.7103 (tp30) REVERT: B 378 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7075 (tp) REVERT: B 401 ASN cc_start: 0.6123 (m110) cc_final: 0.5646 (m-40) REVERT: B 402 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5564 (tp30) REVERT: B 426 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5673 (mtmt) REVERT: B 453 ARG cc_start: 0.6023 (mtm180) cc_final: 0.5522 (ttm-80) REVERT: B 546 GLU cc_start: 0.7967 (tt0) cc_final: 0.7438 (mt-10) REVERT: B 554 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: B 614 LYS cc_start: 0.5555 (OUTLIER) cc_final: 0.5063 (mptp) REVERT: B 624 ASN cc_start: 0.7918 (p0) cc_final: 0.7666 (p0) REVERT: B 662 ARG cc_start: 0.5041 (ttm110) cc_final: 0.4629 (mtm110) REVERT: B 691 CYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6669 (m) REVERT: B 696 LYS cc_start: 0.7347 (tttp) cc_final: 0.6994 (ttpt) REVERT: C 56 THR cc_start: 0.5724 (p) cc_final: 0.4947 (m) REVERT: C 60 LYS cc_start: 0.4928 (mmtm) cc_final: 0.4649 (mmtm) REVERT: C 82 ILE cc_start: 0.5056 (OUTLIER) cc_final: 0.4739 (pp) REVERT: C 110 TYR cc_start: 0.3913 (m-10) cc_final: 0.3534 (m-10) REVERT: C 120 ASP cc_start: 0.0224 (OUTLIER) cc_final: -0.0474 (t0) REVERT: C 322 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.5687 (mmt90) REVERT: C 377 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.6984 (mtm180) REVERT: C 401 ASN cc_start: 0.6107 (m110) cc_final: 0.5607 (m-40) REVERT: C 426 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5599 (mtmt) REVERT: C 470 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7102 (pp20) REVERT: C 478 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: C 505 LYS cc_start: 0.5983 (mtpt) cc_final: 0.5755 (tppp) REVERT: C 546 GLU cc_start: 0.8023 (tt0) cc_final: 0.7495 (mt-10) REVERT: C 561 GLU cc_start: 0.7352 (mp0) cc_final: 0.6886 (tp30) REVERT: C 662 ARG cc_start: 0.5731 (mtp-110) cc_final: 0.4939 (mtm110) REVERT: C 696 LYS cc_start: 0.7224 (tttp) cc_final: 0.6875 (ttpt) REVERT: D 56 THR cc_start: 0.5726 (p) cc_final: 0.4867 (m) REVERT: D 82 ILE cc_start: 0.5101 (OUTLIER) cc_final: 0.4753 (pp) REVERT: D 141 GLU cc_start: 0.2239 (OUTLIER) cc_final: 0.2024 (pt0) REVERT: D 151 ILE cc_start: 0.5859 (OUTLIER) cc_final: 0.5402 (mp) REVERT: D 378 LEU cc_start: 0.7418 (tm) cc_final: 0.6960 (tp) REVERT: D 379 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: D 401 ASN cc_start: 0.6179 (m110) cc_final: 0.5643 (m-40) REVERT: D 402 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5559 (tp30) REVERT: D 453 ARG cc_start: 0.6238 (OUTLIER) cc_final: 0.5788 (ttm-80) REVERT: D 460 ASN cc_start: 0.5429 (OUTLIER) cc_final: 0.5008 (p0) REVERT: D 505 LYS cc_start: 0.5859 (mtpt) cc_final: 0.5358 (tppp) REVERT: D 546 GLU cc_start: 0.7903 (tt0) cc_final: 0.7440 (mt-10) REVERT: D 614 LYS cc_start: 0.5523 (mppt) cc_final: 0.5056 (mptp) REVERT: D 696 LYS cc_start: 0.7206 (tttp) cc_final: 0.6845 (ttpt) REVERT: E 56 THR cc_start: 0.5603 (p) cc_final: 0.4863 (m) REVERT: E 60 LYS cc_start: 0.5131 (mmtm) cc_final: 0.4745 (mmtm) REVERT: E 82 ILE cc_start: 0.5078 (OUTLIER) cc_final: 0.4766 (pp) REVERT: E 126 ILE cc_start: 0.3702 (OUTLIER) cc_final: 0.3438 (tt) REVERT: E 147 ARG cc_start: 0.5591 (ttt-90) cc_final: 0.5170 (ttp-170) REVERT: E 288 LYS cc_start: 0.6505 (ttpp) cc_final: 0.6279 (pttp) REVERT: E 322 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.5766 (mmt90) REVERT: E 366 GLU cc_start: 0.7300 (tt0) cc_final: 0.7081 (tp30) REVERT: E 377 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.7161 (mtm180) REVERT: E 378 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7073 (tp) REVERT: E 401 ASN cc_start: 0.6110 (m110) cc_final: 0.5618 (m-40) REVERT: E 402 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5562 (tp30) REVERT: E 426 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.5745 (mtmt) REVERT: E 449 MET cc_start: 0.6806 (tpt) cc_final: 0.6582 (tpp) REVERT: E 453 ARG cc_start: 0.6009 (mtm180) cc_final: 0.5584 (ttm-80) REVERT: E 546 GLU cc_start: 0.7968 (tt0) cc_final: 0.7439 (mt-10) REVERT: E 554 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: E 614 LYS cc_start: 0.5846 (mtmm) cc_final: 0.5238 (mptp) REVERT: E 691 CYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6672 (m) REVERT: E 696 LYS cc_start: 0.7350 (tttp) cc_final: 0.6983 (ttpt) REVERT: F 56 THR cc_start: 0.5722 (p) cc_final: 0.4947 (m) REVERT: F 60 LYS cc_start: 0.5001 (mmtm) cc_final: 0.4673 (mmtm) REVERT: F 82 ILE cc_start: 0.5053 (OUTLIER) cc_final: 0.4736 (pp) REVERT: F 110 TYR cc_start: 0.3908 (m-10) cc_final: 0.3529 (m-10) REVERT: F 120 ASP cc_start: 0.0221 (OUTLIER) cc_final: -0.0481 (t0) REVERT: F 239 ARG cc_start: 0.6065 (mmm-85) cc_final: 0.5642 (mmm160) REVERT: F 322 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.5809 (mmt90) REVERT: F 402 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.5456 (tp30) REVERT: F 426 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5598 (mtmt) REVERT: F 453 ARG cc_start: 0.5905 (mtm180) cc_final: 0.5516 (ptp-170) REVERT: F 470 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7101 (pp20) REVERT: F 478 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6884 (m-30) REVERT: F 505 LYS cc_start: 0.5990 (mtpt) cc_final: 0.5758 (tppp) REVERT: F 546 GLU cc_start: 0.8022 (tt0) cc_final: 0.7495 (mt-10) REVERT: F 561 GLU cc_start: 0.7349 (mp0) cc_final: 0.6862 (tp30) REVERT: F 662 ARG cc_start: 0.5729 (mtp-110) cc_final: 0.4937 (mtm110) REVERT: F 696 LYS cc_start: 0.7245 (tttp) cc_final: 0.6897 (ttpt) outliers start: 256 outliers final: 146 residues processed: 710 average time/residue: 1.5079 time to fit residues: 1267.0562 Evaluate side-chains 674 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 479 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 750 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 691 CYS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 649 ASP Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 460 ASN Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 327 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN D 616 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34854 Z= 0.220 Angle : 0.698 9.561 47142 Z= 0.342 Chirality : 0.045 0.182 5316 Planarity : 0.005 0.063 6186 Dihedral : 7.847 86.600 4836 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.74 % Favored : 92.12 % Rotamer: Outliers : 5.72 % Allowed : 21.84 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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: -1.86 (0.12), residues: 4314 helix: -0.62 (0.12), residues: 1680 sheet: -0.51 (0.22), residues: 582 loop : -1.96 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 551 HIS 0.004 0.001 HIS F 499 PHE 0.011 0.001 PHE F 758 TYR 0.014 0.002 TYR E 644 ARG 0.011 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 512 time to evaluate : 3.838 Fit side-chains REVERT: A 53 ARG cc_start: 0.3923 (ttm110) cc_final: 0.3355 (ttp-110) REVERT: A 56 THR cc_start: 0.5617 (p) cc_final: 0.4870 (m) REVERT: A 82 ILE cc_start: 0.5125 (OUTLIER) cc_final: 0.4876 (pp) REVERT: A 150 ASP cc_start: 0.4006 (m-30) cc_final: 0.3547 (p0) REVERT: A 291 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5740 (tt0) REVERT: A 322 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.5737 (mmt90) REVERT: A 378 LEU cc_start: 0.7383 (tm) cc_final: 0.6926 (tp) REVERT: A 379 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: A 401 ASN cc_start: 0.6266 (m110) cc_final: 0.5751 (m-40) REVERT: A 402 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5544 (tp30) REVERT: A 426 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.5704 (mtmt) REVERT: A 442 MET cc_start: 0.5374 (OUTLIER) cc_final: 0.5150 (ttp) REVERT: A 449 MET cc_start: 0.6782 (tpt) cc_final: 0.6501 (tpp) REVERT: A 453 ARG cc_start: 0.6294 (mtm110) cc_final: 0.5698 (ttm-80) REVERT: A 460 ASN cc_start: 0.5358 (OUTLIER) cc_final: 0.4967 (p0) REVERT: A 473 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6367 (mm110) REVERT: A 478 ASP cc_start: 0.6965 (m-30) cc_final: 0.6678 (m-30) REVERT: A 505 LYS cc_start: 0.5964 (mtpt) cc_final: 0.5406 (tppp) REVERT: A 546 GLU cc_start: 0.7919 (tt0) cc_final: 0.7542 (mt-10) REVERT: A 614 LYS cc_start: 0.5742 (mtmm) cc_final: 0.5167 (mptp) REVERT: A 662 ARG cc_start: 0.5303 (ttm110) cc_final: 0.4603 (mtm110) REVERT: A 691 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6655 (m) REVERT: A 696 LYS cc_start: 0.7224 (tttp) cc_final: 0.6833 (ttpt) REVERT: B 82 ILE cc_start: 0.4988 (OUTLIER) cc_final: 0.4743 (pp) REVERT: B 126 ILE cc_start: 0.3577 (OUTLIER) cc_final: 0.3071 (tt) REVERT: B 150 ASP cc_start: 0.4129 (m-30) cc_final: 0.3824 (t0) REVERT: B 154 VAL cc_start: 0.5673 (t) cc_final: 0.5452 (t) REVERT: B 210 ARG cc_start: 0.5921 (ttp-110) cc_final: 0.5440 (tpt90) REVERT: B 288 LYS cc_start: 0.6483 (ttpp) cc_final: 0.6247 (pttp) REVERT: B 322 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.5848 (mmt90) REVERT: B 354 ASP cc_start: 0.6078 (t70) cc_final: 0.5862 (t70) REVERT: B 366 GLU cc_start: 0.7248 (tt0) cc_final: 0.7037 (tp30) REVERT: B 378 LEU cc_start: 0.7323 (tm) cc_final: 0.7061 (tp) REVERT: B 401 ASN cc_start: 0.6196 (m110) cc_final: 0.5804 (m-40) REVERT: B 402 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5597 (tp30) REVERT: B 426 LYS cc_start: 0.6389 (OUTLIER) cc_final: 0.5592 (mtmt) REVERT: B 453 ARG cc_start: 0.5951 (mtm180) cc_final: 0.5496 (ttm-80) REVERT: B 546 GLU cc_start: 0.7983 (tt0) cc_final: 0.7545 (mt-10) REVERT: B 614 LYS cc_start: 0.5412 (mtmm) cc_final: 0.5007 (mptp) REVERT: B 624 ASN cc_start: 0.7816 (p0) cc_final: 0.7581 (p0) REVERT: B 662 ARG cc_start: 0.5041 (ttm110) cc_final: 0.4662 (mtm110) REVERT: B 691 CYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6643 (m) REVERT: B 696 LYS cc_start: 0.7286 (tttp) cc_final: 0.6932 (ttpt) REVERT: B 741 ARG cc_start: 0.5905 (mtm-85) cc_final: 0.4681 (mmm-85) REVERT: B 750 ASN cc_start: 0.5191 (OUTLIER) cc_final: 0.4653 (t0) REVERT: C 56 THR cc_start: 0.5532 (p) cc_final: 0.4888 (m) REVERT: C 60 LYS cc_start: 0.4777 (mmtm) cc_final: 0.4509 (mmtm) REVERT: C 82 ILE cc_start: 0.5071 (OUTLIER) cc_final: 0.4819 (pp) REVERT: C 110 TYR cc_start: 0.3914 (m-10) cc_final: 0.3516 (m-10) REVERT: C 120 ASP cc_start: 0.0167 (OUTLIER) cc_final: -0.0442 (t0) REVERT: C 150 ASP cc_start: 0.4128 (m-30) cc_final: 0.3633 (p0) REVERT: C 327 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.5896 (tt0) REVERT: C 377 ARG cc_start: 0.7292 (mtm-85) cc_final: 0.6979 (mtm180) REVERT: C 401 ASN cc_start: 0.6264 (m110) cc_final: 0.5838 (m-40) REVERT: C 426 LYS cc_start: 0.6451 (OUTLIER) cc_final: 0.5562 (mtmt) REVERT: C 449 MET cc_start: 0.6894 (tpt) cc_final: 0.6653 (tpp) REVERT: C 453 ARG cc_start: 0.6460 (mtm110) cc_final: 0.5916 (ttm-80) REVERT: C 478 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: C 505 LYS cc_start: 0.5964 (mtpt) cc_final: 0.5743 (tppp) REVERT: C 546 GLU cc_start: 0.8022 (tt0) cc_final: 0.7509 (mt-10) REVERT: C 561 GLU cc_start: 0.7341 (mp0) cc_final: 0.6855 (tp30) REVERT: C 696 LYS cc_start: 0.7294 (tttp) cc_final: 0.6894 (ttpt) REVERT: C 732 ARG cc_start: 0.4817 (mtm-85) cc_final: 0.4586 (mtm180) REVERT: D 56 THR cc_start: 0.5601 (p) cc_final: 0.4846 (m) REVERT: D 82 ILE cc_start: 0.5080 (OUTLIER) cc_final: 0.4843 (pp) REVERT: D 150 ASP cc_start: 0.4024 (m-30) cc_final: 0.3568 (p0) REVERT: D 378 LEU cc_start: 0.7378 (tm) cc_final: 0.6919 (tp) REVERT: D 379 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: D 401 ASN cc_start: 0.6255 (m110) cc_final: 0.5759 (m-40) REVERT: D 402 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5555 (tp30) REVERT: D 460 ASN cc_start: 0.5318 (OUTLIER) cc_final: 0.4906 (p0) REVERT: D 473 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6320 (mm110) REVERT: D 478 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6791 (m-30) REVERT: D 505 LYS cc_start: 0.5946 (mtpt) cc_final: 0.5401 (tppp) REVERT: D 546 GLU cc_start: 0.7919 (tt0) cc_final: 0.7541 (mt-10) REVERT: D 561 GLU cc_start: 0.7453 (mp0) cc_final: 0.6934 (tp30) REVERT: D 614 LYS cc_start: 0.5288 (mppt) cc_final: 0.5024 (mptp) REVERT: D 691 CYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6650 (m) REVERT: D 696 LYS cc_start: 0.7207 (tttp) cc_final: 0.6826 (ttpt) REVERT: D 750 ASN cc_start: 0.5008 (OUTLIER) cc_final: 0.4542 (t0) REVERT: E 56 THR cc_start: 0.5545 (p) cc_final: 0.4959 (m) REVERT: E 60 LYS cc_start: 0.5065 (mmtm) cc_final: 0.4743 (mmtm) REVERT: E 82 ILE cc_start: 0.5027 (pt) cc_final: 0.4764 (pp) REVERT: E 126 ILE cc_start: 0.3541 (OUTLIER) cc_final: 0.3037 (tt) REVERT: E 288 LYS cc_start: 0.6532 (ttpp) cc_final: 0.6278 (pttp) REVERT: E 322 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5776 (mmt90) REVERT: E 354 ASP cc_start: 0.6067 (t70) cc_final: 0.5825 (t70) REVERT: E 366 GLU cc_start: 0.7245 (tt0) cc_final: 0.7033 (tp30) REVERT: E 377 ARG cc_start: 0.7300 (mtm-85) cc_final: 0.7081 (mtm180) REVERT: E 378 LEU cc_start: 0.7302 (tm) cc_final: 0.7050 (tp) REVERT: E 401 ASN cc_start: 0.6186 (m110) cc_final: 0.5764 (m-40) REVERT: E 402 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5593 (tp30) REVERT: E 426 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.5658 (mtmt) REVERT: E 449 MET cc_start: 0.6779 (tpt) cc_final: 0.6527 (tpp) REVERT: E 453 ARG cc_start: 0.5906 (mtm180) cc_final: 0.5570 (ttm-80) REVERT: E 546 GLU cc_start: 0.7983 (tt0) cc_final: 0.7546 (mt-10) REVERT: E 554 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: E 614 LYS cc_start: 0.5769 (mtmm) cc_final: 0.5206 (mptp) REVERT: E 691 CYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6620 (m) REVERT: E 696 LYS cc_start: 0.7225 (tttp) cc_final: 0.6836 (ttpt) REVERT: E 750 ASN cc_start: 0.5197 (OUTLIER) cc_final: 0.4647 (t0) REVERT: F 56 THR cc_start: 0.5535 (p) cc_final: 0.4892 (m) REVERT: F 60 LYS cc_start: 0.4781 (mmtm) cc_final: 0.4509 (mmtm) REVERT: F 82 ILE cc_start: 0.5069 (OUTLIER) cc_final: 0.4816 (pp) REVERT: F 110 TYR cc_start: 0.3936 (m-10) cc_final: 0.3524 (m-10) REVERT: F 120 ASP cc_start: 0.0169 (OUTLIER) cc_final: -0.0440 (t0) REVERT: F 150 ASP cc_start: 0.4131 (m-30) cc_final: 0.3637 (p0) REVERT: F 239 ARG cc_start: 0.5991 (mmm-85) cc_final: 0.5576 (mmm160) REVERT: F 327 GLN cc_start: 0.6050 (OUTLIER) cc_final: 0.5679 (tt0) REVERT: F 401 ASN cc_start: 0.6369 (m-40) cc_final: 0.5932 (m110) REVERT: F 402 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5475 (tp30) REVERT: F 426 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.5551 (mtmt) REVERT: F 453 ARG cc_start: 0.5962 (mtm180) cc_final: 0.5567 (ptp-170) REVERT: F 478 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6894 (m-30) REVERT: F 505 LYS cc_start: 0.5962 (mtpt) cc_final: 0.5739 (tppp) REVERT: F 546 GLU cc_start: 0.8023 (tt0) cc_final: 0.7509 (mt-10) REVERT: F 561 GLU cc_start: 0.7339 (mp0) cc_final: 0.6849 (tp30) REVERT: F 696 LYS cc_start: 0.7292 (tttp) cc_final: 0.6895 (ttpt) outliers start: 211 outliers final: 111 residues processed: 687 average time/residue: 1.5964 time to fit residues: 1290.6595 Evaluate side-chains 619 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 465 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 750 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 691 CYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 750 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 554 GLU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 649 ASP Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 750 ASN Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 3.9990 chunk 398 optimal weight: 6.9990 chunk 363 optimal weight: 10.0000 chunk 388 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 304 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 350 optimal weight: 0.8980 chunk 366 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN F 340 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34854 Z= 0.236 Angle : 0.713 9.605 47142 Z= 0.349 Chirality : 0.046 0.178 5316 Planarity : 0.005 0.066 6186 Dihedral : 7.853 88.052 4836 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.90 % Favored : 91.96 % Rotamer: Outliers : 5.37 % Allowed : 22.93 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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: -1.78 (0.12), residues: 4314 helix: -0.60 (0.12), residues: 1692 sheet: -0.43 (0.22), residues: 582 loop : -1.89 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 551 HIS 0.004 0.001 HIS C 499 PHE 0.011 0.001 PHE F 758 TYR 0.013 0.002 TYR A 495 ARG 0.010 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 476 time to evaluate : 3.722 Fit side-chains REVERT: A 56 THR cc_start: 0.5634 (p) cc_final: 0.4922 (m) REVERT: A 82 ILE cc_start: 0.5120 (OUTLIER) cc_final: 0.4851 (pp) REVERT: A 236 LYS cc_start: 0.6290 (mptt) cc_final: 0.5991 (mtpt) REVERT: A 322 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.5706 (mmt90) REVERT: A 378 LEU cc_start: 0.7426 (tm) cc_final: 0.6951 (tp) REVERT: A 379 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: A 401 ASN cc_start: 0.6254 (m110) cc_final: 0.5738 (m-40) REVERT: A 402 GLU cc_start: 0.6053 (OUTLIER) cc_final: 0.5548 (tp30) REVERT: A 426 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.5718 (mtmt) REVERT: A 442 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.5139 (ttp) REVERT: A 449 MET cc_start: 0.6754 (tpt) cc_final: 0.6493 (tpp) REVERT: A 453 ARG cc_start: 0.6318 (mtm110) cc_final: 0.5758 (ttm-80) REVERT: A 460 ASN cc_start: 0.5366 (OUTLIER) cc_final: 0.4950 (p0) REVERT: A 470 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: A 473 GLN cc_start: 0.6615 (OUTLIER) cc_final: 0.6377 (mm110) REVERT: A 478 ASP cc_start: 0.6977 (m-30) cc_final: 0.6680 (m-30) REVERT: A 505 LYS cc_start: 0.5944 (mtpt) cc_final: 0.5380 (tppp) REVERT: A 546 GLU cc_start: 0.7917 (tt0) cc_final: 0.7545 (mt-10) REVERT: A 614 LYS cc_start: 0.5765 (mtmm) cc_final: 0.5188 (mptp) REVERT: A 662 ARG cc_start: 0.5274 (ttm110) cc_final: 0.4757 (mtm110) REVERT: A 691 CYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6637 (m) REVERT: A 696 LYS cc_start: 0.7214 (tttp) cc_final: 0.6826 (ttpt) REVERT: B 82 ILE cc_start: 0.5035 (OUTLIER) cc_final: 0.4761 (pp) REVERT: B 110 TYR cc_start: 0.3758 (m-10) cc_final: 0.3089 (m-10) REVERT: B 126 ILE cc_start: 0.3536 (OUTLIER) cc_final: 0.3028 (tt) REVERT: B 154 VAL cc_start: 0.5679 (t) cc_final: 0.5454 (t) REVERT: B 210 ARG cc_start: 0.5905 (ttp-110) cc_final: 0.5388 (tpt90) REVERT: B 288 LYS cc_start: 0.6466 (ttpp) cc_final: 0.6237 (pttp) REVERT: B 322 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5815 (mmt90) REVERT: B 354 ASP cc_start: 0.6110 (t70) cc_final: 0.5894 (t70) REVERT: B 366 GLU cc_start: 0.7253 (tt0) cc_final: 0.7039 (tp30) REVERT: B 378 LEU cc_start: 0.7320 (tm) cc_final: 0.7053 (tp) REVERT: B 401 ASN cc_start: 0.6185 (m110) cc_final: 0.5788 (m-40) REVERT: B 402 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5616 (tp30) REVERT: B 426 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.5605 (mtmt) REVERT: B 453 ARG cc_start: 0.6001 (mtm180) cc_final: 0.5531 (ttm-80) REVERT: B 546 GLU cc_start: 0.7983 (tt0) cc_final: 0.7540 (mt-10) REVERT: B 614 LYS cc_start: 0.5368 (mtmm) cc_final: 0.4968 (mptp) REVERT: B 624 ASN cc_start: 0.7789 (p0) cc_final: 0.7482 (m-40) REVERT: B 662 ARG cc_start: 0.5043 (ttm110) cc_final: 0.4665 (mtm110) REVERT: B 691 CYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6629 (m) REVERT: B 696 LYS cc_start: 0.7247 (tttp) cc_final: 0.6880 (ttpt) REVERT: B 751 ASP cc_start: 0.5989 (OUTLIER) cc_final: 0.5763 (p0) REVERT: C 56 THR cc_start: 0.5544 (p) cc_final: 0.4902 (m) REVERT: C 60 LYS cc_start: 0.4798 (mmtm) cc_final: 0.4523 (mmtm) REVERT: C 82 ILE cc_start: 0.5090 (OUTLIER) cc_final: 0.4810 (pp) REVERT: C 110 TYR cc_start: 0.3971 (m-10) cc_final: 0.3504 (m-10) REVERT: C 120 ASP cc_start: 0.0151 (OUTLIER) cc_final: -0.0469 (t0) REVERT: C 150 ASP cc_start: 0.4225 (m-30) cc_final: 0.3681 (p0) REVERT: C 377 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.6959 (mtm180) REVERT: C 401 ASN cc_start: 0.6251 (m110) cc_final: 0.5791 (m-40) REVERT: C 426 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.5595 (mtmt) REVERT: C 449 MET cc_start: 0.6880 (tpt) cc_final: 0.6632 (tpp) REVERT: C 453 ARG cc_start: 0.6400 (mtm110) cc_final: 0.5855 (ttm-80) REVERT: C 470 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7053 (pp20) REVERT: C 478 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: C 505 LYS cc_start: 0.5992 (mtpt) cc_final: 0.5713 (tppp) REVERT: C 546 GLU cc_start: 0.8015 (tt0) cc_final: 0.7485 (mt-10) REVERT: C 561 GLU cc_start: 0.7339 (mp0) cc_final: 0.6863 (tp30) REVERT: C 696 LYS cc_start: 0.7290 (tttp) cc_final: 0.6930 (ttpt) REVERT: C 732 ARG cc_start: 0.4828 (mtm-85) cc_final: 0.4618 (mtm180) REVERT: D 56 THR cc_start: 0.5650 (p) cc_final: 0.4903 (m) REVERT: D 82 ILE cc_start: 0.5099 (OUTLIER) cc_final: 0.4844 (pp) REVERT: D 291 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5767 (tt0) REVERT: D 327 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5882 (tm-30) REVERT: D 378 LEU cc_start: 0.7431 (tm) cc_final: 0.6959 (tp) REVERT: D 379 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: D 401 ASN cc_start: 0.6238 (m110) cc_final: 0.5740 (m-40) REVERT: D 402 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5583 (tp30) REVERT: D 460 ASN cc_start: 0.5358 (OUTLIER) cc_final: 0.4948 (p0) REVERT: D 473 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6322 (mm110) REVERT: D 478 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: D 505 LYS cc_start: 0.5938 (mtpt) cc_final: 0.5377 (tppp) REVERT: D 546 GLU cc_start: 0.7908 (tt0) cc_final: 0.7539 (mt-10) REVERT: D 561 GLU cc_start: 0.7490 (mp0) cc_final: 0.6974 (tp30) REVERT: D 614 LYS cc_start: 0.5343 (mppt) cc_final: 0.5037 (mptp) REVERT: D 691 CYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6625 (m) REVERT: D 696 LYS cc_start: 0.7217 (tttp) cc_final: 0.6831 (ttpt) REVERT: E 56 THR cc_start: 0.5583 (p) cc_final: 0.4990 (m) REVERT: E 60 LYS cc_start: 0.5044 (mmtm) cc_final: 0.4709 (mmtm) REVERT: E 82 ILE cc_start: 0.5045 (OUTLIER) cc_final: 0.4768 (pp) REVERT: E 126 ILE cc_start: 0.3569 (OUTLIER) cc_final: 0.3031 (tt) REVERT: E 288 LYS cc_start: 0.6518 (ttpp) cc_final: 0.6299 (pttp) REVERT: E 322 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.5762 (mmt90) REVERT: E 354 ASP cc_start: 0.6053 (t70) cc_final: 0.5806 (t70) REVERT: E 366 GLU cc_start: 0.7254 (tt0) cc_final: 0.7036 (tp30) REVERT: E 377 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.7083 (mtm180) REVERT: E 378 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7005 (tp) REVERT: E 401 ASN cc_start: 0.6178 (m110) cc_final: 0.5744 (m-40) REVERT: E 402 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5619 (tp30) REVERT: E 426 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.5654 (mtmt) REVERT: E 449 MET cc_start: 0.6778 (tpt) cc_final: 0.6535 (tpp) REVERT: E 453 ARG cc_start: 0.5924 (mtm180) cc_final: 0.5582 (ttm-80) REVERT: E 546 GLU cc_start: 0.7977 (tt0) cc_final: 0.7538 (mt-10) REVERT: E 614 LYS cc_start: 0.5752 (mtmm) cc_final: 0.5191 (mptp) REVERT: E 691 CYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6619 (m) REVERT: E 696 LYS cc_start: 0.7191 (tttp) cc_final: 0.6818 (ttpt) REVERT: F 46 MET cc_start: 0.2368 (OUTLIER) cc_final: 0.2043 (ppp) REVERT: F 56 THR cc_start: 0.5558 (p) cc_final: 0.4914 (m) REVERT: F 60 LYS cc_start: 0.4797 (mmtm) cc_final: 0.4521 (mmtm) REVERT: F 82 ILE cc_start: 0.5089 (OUTLIER) cc_final: 0.4808 (pp) REVERT: F 110 TYR cc_start: 0.3979 (m-10) cc_final: 0.3498 (m-10) REVERT: F 120 ASP cc_start: 0.0151 (OUTLIER) cc_final: -0.0469 (t0) REVERT: F 150 ASP cc_start: 0.4230 (m-30) cc_final: 0.3687 (p0) REVERT: F 239 ARG cc_start: 0.5974 (mmm-85) cc_final: 0.5573 (mmm160) REVERT: F 401 ASN cc_start: 0.6329 (m-40) cc_final: 0.5854 (m-40) REVERT: F 402 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5387 (tp30) REVERT: F 426 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.5604 (mtmt) REVERT: F 453 ARG cc_start: 0.5911 (mtm180) cc_final: 0.5525 (ptp-170) REVERT: F 470 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7050 (pp20) REVERT: F 478 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: F 505 LYS cc_start: 0.5988 (mtpt) cc_final: 0.5700 (tppp) REVERT: F 546 GLU cc_start: 0.8012 (tt0) cc_final: 0.7479 (mt-10) REVERT: F 561 GLU cc_start: 0.7352 (mp0) cc_final: 0.6851 (tp30) REVERT: F 696 LYS cc_start: 0.7277 (tttp) cc_final: 0.6922 (ttpt) outliers start: 198 outliers final: 114 residues processed: 641 average time/residue: 1.5619 time to fit residues: 1180.1891 Evaluate side-chains 625 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 466 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 751 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 691 CYS Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 649 ASP Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 649 ASP Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 0.9990 chunk 410 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 430 optimal weight: 7.9990 chunk 396 optimal weight: 10.0000 chunk 342 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 536 GLN B 568 GLN B 750 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN D 536 GLN D 568 GLN D 750 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN E 536 GLN E 568 GLN E 750 ASN F 340 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34854 Z= 0.281 Angle : 0.761 9.500 47142 Z= 0.375 Chirality : 0.047 0.188 5316 Planarity : 0.006 0.081 6186 Dihedral : 8.141 92.950 4836 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.44 % Favored : 91.42 % Rotamer: Outliers : 4.96 % Allowed : 23.25 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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: -2.02 (0.12), residues: 4314 helix: -0.85 (0.12), residues: 1722 sheet: -0.96 (0.20), residues: 660 loop : -1.87 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 551 HIS 0.004 0.001 HIS F 384 PHE 0.019 0.002 PHE A 267 TYR 0.017 0.002 TYR A 495 ARG 0.012 0.001 ARG A 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 492 time to evaluate : 3.808 Fit side-chains REVERT: A 56 THR cc_start: 0.5519 (p) cc_final: 0.4766 (m) REVERT: A 68 VAL cc_start: 0.4981 (p) cc_final: 0.4719 (t) REVERT: A 82 ILE cc_start: 0.5095 (OUTLIER) cc_final: 0.4757 (pp) REVERT: A 322 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.5788 (mmt90) REVERT: A 378 LEU cc_start: 0.7447 (tm) cc_final: 0.6959 (tp) REVERT: A 379 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: A 401 ASN cc_start: 0.6189 (m110) cc_final: 0.5682 (m-40) REVERT: A 402 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5543 (tp30) REVERT: A 417 GLU cc_start: 0.7768 (tt0) cc_final: 0.7339 (tp30) REVERT: A 426 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.5735 (mtmt) REVERT: A 442 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.5159 (ttp) REVERT: A 449 MET cc_start: 0.6757 (tpt) cc_final: 0.6500 (tpp) REVERT: A 453 ARG cc_start: 0.6290 (mtm110) cc_final: 0.5743 (ttm-80) REVERT: A 460 ASN cc_start: 0.5389 (OUTLIER) cc_final: 0.4986 (p0) REVERT: A 470 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: A 473 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6360 (mm110) REVERT: A 478 ASP cc_start: 0.6986 (m-30) cc_final: 0.6686 (m-30) REVERT: A 505 LYS cc_start: 0.5900 (mtpt) cc_final: 0.5319 (tppp) REVERT: A 546 GLU cc_start: 0.7932 (tt0) cc_final: 0.7464 (mt-10) REVERT: A 614 LYS cc_start: 0.5821 (mtmm) cc_final: 0.5222 (mptp) REVERT: A 662 ARG cc_start: 0.5278 (ttm110) cc_final: 0.4739 (mtm110) REVERT: A 691 CYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6653 (m) REVERT: A 696 LYS cc_start: 0.7238 (tttp) cc_final: 0.6849 (ttpt) REVERT: A 740 MET cc_start: 0.7447 (tpp) cc_final: 0.6767 (mmm) REVERT: B 68 VAL cc_start: 0.4921 (p) cc_final: 0.4714 (t) REVERT: B 82 ILE cc_start: 0.5050 (OUTLIER) cc_final: 0.4771 (pp) REVERT: B 110 TYR cc_start: 0.3815 (m-10) cc_final: 0.3114 (m-10) REVERT: B 126 ILE cc_start: 0.3575 (OUTLIER) cc_final: 0.3050 (tt) REVERT: B 150 ASP cc_start: 0.4178 (m-30) cc_final: 0.3592 (p0) REVERT: B 154 VAL cc_start: 0.5639 (t) cc_final: 0.5427 (t) REVERT: B 210 ARG cc_start: 0.5936 (ttp-110) cc_final: 0.5321 (tmt-80) REVERT: B 288 LYS cc_start: 0.6511 (ttpp) cc_final: 0.6306 (pttp) REVERT: B 322 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.5792 (mmt90) REVERT: B 366 GLU cc_start: 0.7278 (tt0) cc_final: 0.7074 (tp30) REVERT: B 378 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7064 (tp) REVERT: B 401 ASN cc_start: 0.6155 (m110) cc_final: 0.5709 (m-40) REVERT: B 402 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5553 (tp30) REVERT: B 426 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.5629 (mtmt) REVERT: B 453 ARG cc_start: 0.5988 (mtm180) cc_final: 0.5498 (ttm-80) REVERT: B 546 GLU cc_start: 0.7972 (tt0) cc_final: 0.7509 (mt-10) REVERT: B 614 LYS cc_start: 0.5362 (mtmm) cc_final: 0.4961 (mptp) REVERT: B 624 ASN cc_start: 0.7844 (p0) cc_final: 0.7590 (p0) REVERT: B 662 ARG cc_start: 0.5093 (ttm110) cc_final: 0.4675 (mtm110) REVERT: B 691 CYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6638 (m) REVERT: B 696 LYS cc_start: 0.7253 (tttp) cc_final: 0.6821 (ttpt) REVERT: B 741 ARG cc_start: 0.5928 (mtm-85) cc_final: 0.4715 (mmm-85) REVERT: C 46 MET cc_start: 0.2435 (mmp) cc_final: 0.2005 (ppp) REVERT: C 56 THR cc_start: 0.5663 (p) cc_final: 0.4998 (m) REVERT: C 60 LYS cc_start: 0.4888 (mmtm) cc_final: 0.4626 (mmtm) REVERT: C 82 ILE cc_start: 0.5094 (OUTLIER) cc_final: 0.4791 (pp) REVERT: C 110 TYR cc_start: 0.4016 (m-10) cc_final: 0.3541 (m-10) REVERT: C 120 ASP cc_start: 0.0098 (OUTLIER) cc_final: -0.0517 (t0) REVERT: C 150 ASP cc_start: 0.4164 (m-30) cc_final: 0.3607 (p0) REVERT: C 401 ASN cc_start: 0.6200 (m110) cc_final: 0.5737 (m-40) REVERT: C 426 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.5657 (mtmt) REVERT: C 453 ARG cc_start: 0.6431 (mtm110) cc_final: 0.5828 (ptp-170) REVERT: C 470 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: C 478 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: C 505 LYS cc_start: 0.6063 (mtpt) cc_final: 0.5721 (tppp) REVERT: C 546 GLU cc_start: 0.8032 (tt0) cc_final: 0.7494 (mt-10) REVERT: C 561 GLU cc_start: 0.7321 (mp0) cc_final: 0.6846 (tp30) REVERT: C 696 LYS cc_start: 0.7296 (tttp) cc_final: 0.6930 (ttpt) REVERT: C 732 ARG cc_start: 0.4784 (mtm-85) cc_final: 0.4433 (mtm180) REVERT: C 738 GLU cc_start: 0.5788 (tp30) cc_final: 0.5567 (tp30) REVERT: D 56 THR cc_start: 0.5660 (p) cc_final: 0.4894 (m) REVERT: D 68 VAL cc_start: 0.4964 (p) cc_final: 0.4699 (t) REVERT: D 82 ILE cc_start: 0.5116 (OUTLIER) cc_final: 0.4757 (pp) REVERT: D 379 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: D 401 ASN cc_start: 0.6185 (m110) cc_final: 0.5671 (m-40) REVERT: D 402 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5543 (tp30) REVERT: D 460 ASN cc_start: 0.5385 (OUTLIER) cc_final: 0.5002 (p0) REVERT: D 470 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7212 (pp20) REVERT: D 473 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.6281 (mm110) REVERT: D 478 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6792 (m-30) REVERT: D 505 LYS cc_start: 0.5871 (mtpt) cc_final: 0.5296 (tppp) REVERT: D 546 GLU cc_start: 0.7928 (tt0) cc_final: 0.7459 (mt-10) REVERT: D 561 GLU cc_start: 0.7503 (mp0) cc_final: 0.6970 (tp30) REVERT: D 614 LYS cc_start: 0.5341 (mppt) cc_final: 0.4985 (mptp) REVERT: D 691 CYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6633 (m) REVERT: D 696 LYS cc_start: 0.7242 (tttp) cc_final: 0.6854 (ttpt) REVERT: D 740 MET cc_start: 0.7436 (tpp) cc_final: 0.6754 (mmm) REVERT: E 60 LYS cc_start: 0.5118 (mmtm) cc_final: 0.4749 (mmtm) REVERT: E 82 ILE cc_start: 0.5060 (OUTLIER) cc_final: 0.4784 (pp) REVERT: E 126 ILE cc_start: 0.3566 (OUTLIER) cc_final: 0.3031 (tt) REVERT: E 288 LYS cc_start: 0.6484 (ttpp) cc_final: 0.6270 (pttp) REVERT: E 322 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.5776 (mmt90) REVERT: E 366 GLU cc_start: 0.7283 (tt0) cc_final: 0.7082 (tp30) REVERT: E 377 ARG cc_start: 0.7360 (mtm-85) cc_final: 0.7075 (mtm180) REVERT: E 378 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7033 (tp) REVERT: E 401 ASN cc_start: 0.6149 (m110) cc_final: 0.5671 (m-40) REVERT: E 402 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.5555 (tp30) REVERT: E 426 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.5702 (mtmt) REVERT: E 449 MET cc_start: 0.6796 (tpt) cc_final: 0.6573 (tpp) REVERT: E 453 ARG cc_start: 0.5964 (mtm180) cc_final: 0.5614 (ttm-80) REVERT: E 478 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: E 546 GLU cc_start: 0.7971 (tt0) cc_final: 0.7509 (mt-10) REVERT: E 614 LYS cc_start: 0.5769 (mtmm) cc_final: 0.5180 (mptp) REVERT: E 691 CYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6624 (m) REVERT: E 696 LYS cc_start: 0.7191 (tttp) cc_final: 0.6823 (ttpt) REVERT: E 751 ASP cc_start: 0.5951 (OUTLIER) cc_final: 0.5748 (p0) REVERT: F 46 MET cc_start: 0.2512 (OUTLIER) cc_final: 0.2041 (ppp) REVERT: F 56 THR cc_start: 0.5644 (p) cc_final: 0.4984 (m) REVERT: F 60 LYS cc_start: 0.4890 (mmtm) cc_final: 0.4628 (mmtm) REVERT: F 82 ILE cc_start: 0.5082 (OUTLIER) cc_final: 0.4785 (pp) REVERT: F 110 TYR cc_start: 0.3999 (m-10) cc_final: 0.3520 (m-10) REVERT: F 120 ASP cc_start: 0.0105 (OUTLIER) cc_final: -0.0510 (t0) REVERT: F 239 ARG cc_start: 0.6018 (mmm-85) cc_final: 0.5586 (mmm160) REVERT: F 401 ASN cc_start: 0.6353 (m-40) cc_final: 0.5882 (m-40) REVERT: F 402 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5493 (tp30) REVERT: F 426 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.5656 (mtmt) REVERT: F 453 ARG cc_start: 0.5895 (mtm180) cc_final: 0.5500 (ptp-170) REVERT: F 470 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7086 (pp20) REVERT: F 478 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6876 (m-30) REVERT: F 505 LYS cc_start: 0.6065 (mtpt) cc_final: 0.5720 (tppp) REVERT: F 546 GLU cc_start: 0.8034 (tt0) cc_final: 0.7495 (mt-10) REVERT: F 561 GLU cc_start: 0.7343 (mp0) cc_final: 0.6854 (tp30) REVERT: F 696 LYS cc_start: 0.7290 (tttp) cc_final: 0.6929 (ttpt) REVERT: F 738 GLU cc_start: 0.5755 (tp30) cc_final: 0.5519 (tp30) outliers start: 183 outliers final: 117 residues processed: 645 average time/residue: 1.5465 time to fit residues: 1182.4664 Evaluate side-chains 635 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 472 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 649 ASP Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 649 ASP Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 270 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 379 GLU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 691 CYS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 219 MET Chi-restraints excluded: chain E residue 270 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 473 GLN Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 649 ASP Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain E residue 691 CYS Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 649 ASP Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain F residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 30.0000 chunk 365 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 316 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 352 optimal weight: 0.0670 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN F 340 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.230009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.204628 restraints weight = 41840.006| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.70 r_work: 0.4137 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34854 Z= 0.274 Angle : 0.756 9.566 47142 Z= 0.372 Chirality : 0.047 0.192 5316 Planarity : 0.006 0.083 6186 Dihedral : 8.114 91.869 4836 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.53 % Favored : 91.33 % Rotamer: Outliers : 5.07 % Allowed : 23.20 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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: -2.01 (0.12), residues: 4314 helix: -0.82 (0.12), residues: 1716 sheet: -0.94 (0.21), residues: 642 loop : -1.87 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 551 HIS 0.004 0.001 HIS C 384 PHE 0.014 0.002 PHE F 758 TYR 0.017 0.002 TYR A 495 ARG 0.012 0.001 ARG A 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17901.85 seconds wall clock time: 313 minutes 43.72 seconds (18823.72 seconds total)