Starting phenix.real_space_refine (version: dev) on Mon Dec 19 05:58:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/12_2022/5ftk_3296_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/12_2022/5ftk_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_3296/12_2022/5ftk_3296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/12_2022/5ftk_3296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/12_2022/5ftk_3296_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ftk_3296/12_2022/5ftk_3296_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 18.64, per 1000 atoms: 0.54 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: 13.01 Conformation dependent library (CDL) restraints added in 4.8 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: 4.56 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: 13.37 Time building geometry restraints manager: 14.17 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 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. 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: 1.600 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: 9.970 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.320 Process input model: 84.080 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 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 : 1.386 14.301 47142 Z= 0.794 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 : 25.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.12 % Favored : 93.46 % Rotamer Outliers : 0.65 % 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 *********************** 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 : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 6 residues processed: 929 average time/residue: 1.6003 time to fit residues: 1743.9759 Evaluate side-chains 471 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 465 time to evaluate : 3.904 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 5.9181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 338 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 205 optimal weight: 0.0770 chunk 252 optimal weight: 7.9990 chunk 392 optimal weight: 6.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 129 ASN A 285 ASN A 536 GLN A 558 ASN A 568 GLN A 616 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN B 285 ASN B 536 GLN B 558 ASN B 568 GLN B 616 ASN B 692 GLN B 750 ASN C 36 ASN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 36 ASN D 129 ASN D 285 ASN D 536 GLN D 558 ASN D 568 GLN D 616 ASN E 36 ASN ** E 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 36 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN F 285 ASN F 536 GLN F 568 GLN F 616 ASN F 692 GLN F 750 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 34854 Z= 0.241 Angle : 0.805 22.572 47142 Z= 0.391 Chirality : 0.048 0.165 5316 Planarity : 0.006 0.059 6186 Dihedral : 8.551 104.020 4836 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 3.50 % 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: -2.83 (0.11), residues: 4314 helix: -1.70 (0.11), residues: 1602 sheet: -1.62 (0.17), residues: 726 loop : -2.02 (0.12), residues: 1986 *********************** 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 722 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 593 time to evaluate : 4.064 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 30 residues processed: 685 average time/residue: 1.5091 time to fit residues: 1228.6292 Evaluate side-chains 520 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 490 time to evaluate : 4.010 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 1.5663 time to fit residues: 13.2588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 326 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 chunk 389 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 536 GLN A 568 GLN A 616 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 558 ASN C 568 GLN C 616 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN D 536 GLN D 568 GLN D 616 ASN D 750 ASN E 317 HIS ** 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 558 ASN F 568 GLN F 616 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 34854 Z= 0.296 Angle : 0.808 20.306 47142 Z= 0.393 Chirality : 0.048 0.168 5316 Planarity : 0.006 0.043 6186 Dihedral : 8.394 92.867 4836 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.68 % Favored : 93.18 % Rotamer Outliers : 4.09 % 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: -2.37 (0.12), residues: 4314 helix: -1.18 (0.11), residues: 1644 sheet: -1.25 (0.18), residues: 678 loop : -1.95 (0.13), residues: 1992 *********************** 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 640 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 489 time to evaluate : 3.945 Fit side-chains outliers start: 151 outliers final: 78 residues processed: 594 average time/residue: 1.4598 time to fit residues: 1036.0419 Evaluate side-chains 521 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 443 time to evaluate : 3.577 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 59 residues processed: 19 average time/residue: 0.4318 time to fit residues: 19.1837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 394 optimal weight: 10.0000 chunk 417 optimal weight: 20.0000 chunk 206 optimal weight: 7.9990 chunk 373 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN A 616 ASN ** 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 ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN D 616 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN F 296 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN F 568 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 34854 Z= 0.343 Angle : 0.835 18.633 47142 Z= 0.408 Chirality : 0.049 0.177 5316 Planarity : 0.006 0.045 6186 Dihedral : 8.604 97.594 4836 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.56 % Favored : 92.30 % Rotamer Outliers : 5.20 % 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: -2.39 (0.12), residues: 4314 helix: -1.11 (0.12), residues: 1644 sheet: -1.22 (0.18), residues: 696 loop : -2.08 (0.13), residues: 1974 *********************** 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 674 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 482 time to evaluate : 4.265 Fit side-chains revert: symmetry clash outliers start: 192 outliers final: 101 residues processed: 622 average time/residue: 1.4844 time to fit residues: 1115.6721 Evaluate side-chains 549 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 448 time to evaluate : 4.260 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 79 residues processed: 22 average time/residue: 0.4810 time to fit residues: 23.0974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 288 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 105 optimal weight: 0.0980 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** 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 443 ASN C 536 GLN C 568 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN F 536 GLN F 568 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.4018 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= 0.237 Angle : 0.731 16.636 47142 Z= 0.352 Chirality : 0.046 0.287 5316 Planarity : 0.005 0.037 6186 Dihedral : 7.998 89.125 4836 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.39 % Favored : 92.47 % Rotamer Outliers : 5.53 % 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: -1.97 (0.12), residues: 4314 helix: -0.76 (0.12), residues: 1662 sheet: -0.52 (0.21), residues: 582 loop : -1.99 (0.13), residues: 2070 *********************** 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 683 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 479 time to evaluate : 3.863 Fit side-chains outliers start: 204 outliers final: 103 residues processed: 657 average time/residue: 1.3823 time to fit residues: 1095.7071 Evaluate side-chains 540 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 437 time to evaluate : 3.842 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 101 residues processed: 2 average time/residue: 0.3431 time to fit residues: 6.8720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 7.9990 chunk 376 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 245 optimal weight: 0.0470 chunk 103 optimal weight: 20.0000 chunk 417 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 overall best weight: 6.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 317 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN B 296 ASN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN B 750 ASN C 296 ASN ** 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 E 296 ASN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN E 750 ASN ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 34854 Z= 0.311 Angle : 0.798 17.374 47142 Z= 0.389 Chirality : 0.049 0.247 5316 Planarity : 0.006 0.054 6186 Dihedral : 8.345 95.721 4836 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.58 % Favored : 92.28 % Rotamer Outliers : 5.96 % 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: -2.09 (0.12), residues: 4314 helix: -0.85 (0.12), residues: 1668 sheet: -1.17 (0.19), residues: 702 loop : -1.88 (0.14), residues: 1944 *********************** 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 686 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 466 time to evaluate : 3.857 Fit side-chains outliers start: 220 outliers final: 123 residues processed: 657 average time/residue: 1.3644 time to fit residues: 1087.2541 Evaluate side-chains 563 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 440 time to evaluate : 3.993 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 113 residues processed: 10 average time/residue: 0.3291 time to fit residues: 11.7049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 238 optimal weight: 0.6980 chunk 305 optimal weight: 30.0000 chunk 236 optimal weight: 5.9990 chunk 351 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 416 optimal weight: 20.0000 chunk 260 optimal weight: 0.0870 chunk 253 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 3.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN A 616 ASN ** 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN E 568 GLN ** F 327 GLN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 34854 Z= 0.218 Angle : 0.714 16.162 47142 Z= 0.344 Chirality : 0.045 0.183 5316 Planarity : 0.005 0.056 6186 Dihedral : 7.748 86.400 4836 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.35 % Favored : 92.51 % Rotamer Outliers : 5.23 % 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: -1.79 (0.12), residues: 4314 helix: -0.68 (0.12), residues: 1728 sheet: -0.94 (0.20), residues: 678 loop : -1.67 (0.14), residues: 1908 *********************** 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 645 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 452 time to evaluate : 4.322 Fit side-chains outliers start: 193 outliers final: 119 residues processed: 622 average time/residue: 1.3324 time to fit residues: 1008.1315 Evaluate side-chains 525 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 406 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 119 residues processed: 0 time to fit residues: 5.1561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 30.0000 chunk 166 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 38 optimal weight: 40.0000 chunk 327 optimal weight: 20.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** 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 327 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN ** 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.4525 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= 0.246 Angle : 0.741 17.044 47142 Z= 0.358 Chirality : 0.046 0.190 5316 Planarity : 0.005 0.054 6186 Dihedral : 7.841 89.371 4836 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.74 % Favored : 92.12 % Rotamer Outliers : 4.82 % 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: -1.82 (0.12), residues: 4314 helix: -0.67 (0.12), residues: 1722 sheet: -0.97 (0.20), residues: 690 loop : -1.72 (0.14), residues: 1902 *********************** 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 607 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 429 time to evaluate : 3.907 Fit side-chains revert: symmetry clash outliers start: 178 outliers final: 129 residues processed: 583 average time/residue: 1.3737 time to fit residues: 968.9550 Evaluate side-chains 536 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 407 time to evaluate : 4.169 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 123 residues processed: 6 average time/residue: 0.3551 time to fit residues: 10.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 0.8980 chunk 398 optimal weight: 20.0000 chunk 363 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 233 optimal weight: 30.0000 chunk 169 optimal weight: 0.7980 chunk 304 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 350 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 386 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN A 536 GLN A 568 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 536 GLN B 568 GLN C 115 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN D 536 GLN D 568 GLN ** 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 Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.4635 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= 0.234 Angle : 0.732 16.547 47142 Z= 0.351 Chirality : 0.046 0.250 5316 Planarity : 0.005 0.054 6186 Dihedral : 7.728 89.257 4836 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.90 % Favored : 91.96 % Rotamer Outliers : 4.07 % 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: -1.76 (0.12), residues: 4314 helix: -0.60 (0.12), residues: 1722 sheet: -0.89 (0.20), residues: 678 loop : -1.72 (0.14), residues: 1914 *********************** 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 569 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 419 time to evaluate : 3.919 Fit side-chains outliers start: 150 outliers final: 127 residues processed: 562 average time/residue: 1.4223 time to fit residues: 966.8731 Evaluate side-chains 526 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 399 time to evaluate : 3.938 Switching outliers to nearest non-outliers outliers start: 127 outliers final: 125 residues processed: 2 average time/residue: 0.4032 time to fit residues: 7.8121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 20.0000 chunk 410 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 430 optimal weight: 6.9990 chunk 396 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN D 296 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 34854 Z= 0.320 Angle : 0.820 17.814 47142 Z= 0.398 Chirality : 0.049 0.241 5316 Planarity : 0.006 0.060 6186 Dihedral : 8.244 97.858 4836 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.07 % Favored : 91.79 % Rotamer Outliers : 4.20 % 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: -0.76 (0.12), residues: 1680 sheet: -1.01 (0.19), residues: 696 loop : -1.92 (0.13), residues: 1938 ********************** 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 574 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 419 time to evaluate : 4.010 Fit side-chains outliers start: 155 outliers final: 114 residues processed: 564 average time/residue: 1.3856 time to fit residues: 948.2202 Evaluate side-chains 518 residues out of total 3690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 404 time to evaluate : 3.990 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 112 residues processed: 2 average time/residue: 0.2977 time to fit residues: 6.8164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 5.9990 chunk 365 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 316 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN B 568 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 568 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN ** 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.230333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.204612 restraints weight = 41641.359| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 1.54 r_work: 0.4146 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4705 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= 0.272 Angle : 0.775 16.853 47142 Z= 0.375 Chirality : 0.047 0.238 5316 Planarity : 0.006 0.062 6186 Dihedral : 8.062 97.353 4836 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.62 % Favored : 91.26 % Rotamer Outliers : 3.79 % 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: -1.94 (0.12), residues: 4314 helix: -0.70 (0.12), residues: 1686 sheet: -0.93 (0.20), residues: 678 loop : -1.89 (0.13), residues: 1950 =============================================================================== Job complete usr+sys time: 15453.54 seconds wall clock time: 271 minutes 18.94 seconds (16278.94 seconds total)