Starting phenix.real_space_refine on Tue Nov 19 04:57:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/11_2024/8io6_35609.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/11_2024/8io6_35609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/11_2024/8io6_35609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/11_2024/8io6_35609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/11_2024/8io6_35609.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/11_2024/8io6_35609.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 160 5.16 5 C 32664 2.51 5 N 8776 2.21 5 O 9880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 272 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51504 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "B" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "C" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "D" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "E" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "F" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "G" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "H" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.46, per 1000 atoms: 0.51 Number of scatterers: 51504 At special positions: 0 Unit cell: (186.75, 186.75, 115.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 P 16 15.00 Mg 8 11.99 O 9880 8.00 N 8776 7.00 C 32664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.72 Conformation dependent library (CDL) restraints added in 6.3 seconds 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11920 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 56 sheets defined 50.1% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.39 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.516A pdb=" N LEU A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.762A pdb=" N GLY A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.607A pdb=" N GLU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.504A pdb=" N HIS A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.667A pdb=" N LYS A 198 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 removed outlier: 3.706A pdb=" N ILE A 228 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 240 removed outlier: 3.523A pdb=" N MET A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 284 removed outlier: 4.081A pdb=" N THR A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.689A pdb=" N SER A 319 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 removed outlier: 3.642A pdb=" N PHE A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.829A pdb=" N LEU A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.529A pdb=" N LEU A 369 " --> pdb=" O LYS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.121A pdb=" N ILE A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 383' Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 397 through 403 removed outlier: 3.769A pdb=" N GLU A 401 " --> pdb=" O LYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.820A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.563A pdb=" N SER A 446 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 526 removed outlier: 3.529A pdb=" N ILE A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.524A pdb=" N ARG A 545 " --> pdb=" O HIS A 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 546 " --> pdb=" O VAL A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 546' Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 557 through 564 removed outlier: 3.524A pdb=" N VAL A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 Processing helix chain 'A' and resid 613 through 624 removed outlier: 4.174A pdb=" N LYS A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 665 removed outlier: 3.505A pdb=" N GLU A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 removed outlier: 3.553A pdb=" N SER A 679 " --> pdb=" O ASP A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'A' and resid 742 through 749 removed outlier: 3.609A pdb=" N VAL A 747 " --> pdb=" O PRO A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 766 Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.596A pdb=" N ASP A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 800 Processing helix chain 'B' and resid 18 through 42 removed outlier: 3.516A pdb=" N LEU B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 86 Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.761A pdb=" N GLY B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 removed outlier: 3.607A pdb=" N GLU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.504A pdb=" N HIS B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 187 through 194 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.667A pdb=" N LYS B 198 " --> pdb=" O GLN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.706A pdb=" N ILE B 228 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.524A pdb=" N MET B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 284 removed outlier: 4.081A pdb=" N THR B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.689A pdb=" N SER B 319 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 343 removed outlier: 3.642A pdb=" N PHE B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.828A pdb=" N LEU B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.528A pdb=" N LEU B 369 " --> pdb=" O LYS B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 removed outlier: 4.122A pdb=" N ILE B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 383' Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 397 through 403 removed outlier: 3.769A pdb=" N GLU B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.820A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 removed outlier: 3.563A pdb=" N SER B 446 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 492 Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'B' and resid 508 through 526 removed outlier: 3.529A pdb=" N ILE B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.525A pdb=" N ARG B 545 " --> pdb=" O HIS B 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 546 " --> pdb=" O VAL B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 557 through 564 removed outlier: 3.524A pdb=" N VAL B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 613 through 624 removed outlier: 4.174A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 665 removed outlier: 3.506A pdb=" N GLU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 665 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.553A pdb=" N SER B 679 " --> pdb=" O ASP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 699 Processing helix chain 'B' and resid 713 through 718 Processing helix chain 'B' and resid 742 through 749 removed outlier: 3.609A pdb=" N VAL B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 766 Processing helix chain 'B' and resid 770 through 792 removed outlier: 3.597A pdb=" N ASP B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 Processing helix chain 'C' and resid 18 through 42 removed outlier: 3.515A pdb=" N LEU C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 67 through 86 Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.761A pdb=" N GLY C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 116 removed outlier: 3.607A pdb=" N GLU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.504A pdb=" N HIS C 163 " --> pdb=" O TYR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 186 Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'C' and resid 195 through 199 removed outlier: 3.668A pdb=" N LYS C 198 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.707A pdb=" N ILE C 228 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 240 removed outlier: 3.524A pdb=" N MET C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 284 removed outlier: 4.081A pdb=" N THR C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.689A pdb=" N SER C 319 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 343 removed outlier: 3.643A pdb=" N PHE C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.828A pdb=" N LEU C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.529A pdb=" N LEU C 369 " --> pdb=" O LYS C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 removed outlier: 4.122A pdb=" N ILE C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 383' Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 397 through 403 removed outlier: 3.770A pdb=" N GLU C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 426 removed outlier: 3.822A pdb=" N LEU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 removed outlier: 3.562A pdb=" N SER C 446 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 504 through 507 Processing helix chain 'C' and resid 508 through 526 removed outlier: 3.529A pdb=" N ILE C 526 " --> pdb=" O THR C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.526A pdb=" N ARG C 545 " --> pdb=" O HIS C 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 546 " --> pdb=" O VAL C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 546' Processing helix chain 'C' and resid 550 through 554 Processing helix chain 'C' and resid 557 through 564 removed outlier: 3.523A pdb=" N VAL C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 Processing helix chain 'C' and resid 613 through 624 removed outlier: 4.174A pdb=" N LYS C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 665 removed outlier: 3.506A pdb=" N GLU C 664 " --> pdb=" O ASP C 660 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 665 " --> pdb=" O LYS C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 681 removed outlier: 3.552A pdb=" N SER C 679 " --> pdb=" O ASP C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 699 Processing helix chain 'C' and resid 713 through 718 Processing helix chain 'C' and resid 742 through 749 removed outlier: 3.609A pdb=" N VAL C 747 " --> pdb=" O PRO C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 766 Processing helix chain 'C' and resid 770 through 792 removed outlier: 3.596A pdb=" N ASP C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 800 Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.515A pdb=" N LEU D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 67 through 86 Processing helix chain 'D' and resid 98 through 109 removed outlier: 3.761A pdb=" N GLY D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 removed outlier: 3.607A pdb=" N GLU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 159 through 169 removed outlier: 3.504A pdb=" N HIS D 163 " --> pdb=" O TYR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 186 Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'D' and resid 195 through 199 removed outlier: 3.668A pdb=" N LYS D 198 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 removed outlier: 3.706A pdb=" N ILE D 228 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 240 removed outlier: 3.523A pdb=" N MET D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 284 removed outlier: 4.082A pdb=" N THR D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 removed outlier: 3.689A pdb=" N SER D 319 " --> pdb=" O SER D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 343 removed outlier: 3.643A pdb=" N PHE D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 removed outlier: 3.829A pdb=" N LEU D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 366 through 370 removed outlier: 3.529A pdb=" N LEU D 369 " --> pdb=" O LYS D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 383 removed outlier: 4.122A pdb=" N ILE D 382 " --> pdb=" O ASN D 378 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 378 through 383' Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.769A pdb=" N GLU D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 426 removed outlier: 3.821A pdb=" N LEU D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 removed outlier: 3.562A pdb=" N SER D 446 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 492 Processing helix chain 'D' and resid 504 through 507 Processing helix chain 'D' and resid 508 through 526 removed outlier: 3.530A pdb=" N ILE D 526 " --> pdb=" O THR D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.524A pdb=" N ARG D 545 " --> pdb=" O HIS D 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D 546 " --> pdb=" O VAL D 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 546' Processing helix chain 'D' and resid 550 through 554 Processing helix chain 'D' and resid 557 through 564 removed outlier: 3.524A pdb=" N VAL D 561 " --> pdb=" O GLY D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 594 Processing helix chain 'D' and resid 613 through 624 removed outlier: 4.174A pdb=" N LYS D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 665 removed outlier: 3.506A pdb=" N GLU D 664 " --> pdb=" O ASP D 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 665 " --> pdb=" O LYS D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 681 removed outlier: 3.552A pdb=" N SER D 679 " --> pdb=" O ASP D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 699 Processing helix chain 'D' and resid 713 through 718 Processing helix chain 'D' and resid 742 through 749 removed outlier: 3.609A pdb=" N VAL D 747 " --> pdb=" O PRO D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 766 Processing helix chain 'D' and resid 770 through 792 removed outlier: 3.597A pdb=" N ASP D 782 " --> pdb=" O GLU D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 800 Processing helix chain 'E' and resid 18 through 42 removed outlier: 3.515A pdb=" N LEU E 22 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 40 " --> pdb=" O SER E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 67 through 86 Processing helix chain 'E' and resid 98 through 109 removed outlier: 3.762A pdb=" N GLY E 102 " --> pdb=" O GLY E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 116 removed outlier: 3.607A pdb=" N GLU E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.504A pdb=" N HIS E 163 " --> pdb=" O TYR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 186 Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'E' and resid 195 through 199 removed outlier: 3.667A pdb=" N LYS E 198 " --> pdb=" O GLN E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 removed outlier: 3.706A pdb=" N ILE E 228 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 240 removed outlier: 3.523A pdb=" N MET E 240 " --> pdb=" O PHE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 284 removed outlier: 4.082A pdb=" N THR E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 320 removed outlier: 3.689A pdb=" N SER E 319 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 343 removed outlier: 3.642A pdb=" N PHE E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 removed outlier: 3.829A pdb=" N LEU E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 366 through 370 removed outlier: 3.529A pdb=" N LEU E 369 " --> pdb=" O LYS E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 383 removed outlier: 4.121A pdb=" N ILE E 382 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG E 383 " --> pdb=" O GLY E 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 378 through 383' Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 397 through 403 removed outlier: 3.769A pdb=" N GLU E 401 " --> pdb=" O LYS E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 426 removed outlier: 3.821A pdb=" N LEU E 415 " --> pdb=" O ALA E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 449 removed outlier: 3.562A pdb=" N SER E 446 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 492 Processing helix chain 'E' and resid 504 through 507 Processing helix chain 'E' and resid 508 through 526 removed outlier: 3.529A pdb=" N ILE E 526 " --> pdb=" O THR E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 546 removed outlier: 3.525A pdb=" N ARG E 545 " --> pdb=" O HIS E 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN E 546 " --> pdb=" O VAL E 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 542 through 546' Processing helix chain 'E' and resid 550 through 554 Processing helix chain 'E' and resid 557 through 564 removed outlier: 3.524A pdb=" N VAL E 561 " --> pdb=" O GLY E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 594 Processing helix chain 'E' and resid 613 through 624 removed outlier: 4.175A pdb=" N LYS E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 665 removed outlier: 3.507A pdb=" N GLU E 664 " --> pdb=" O ASP E 660 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 665 " --> pdb=" O LYS E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 681 removed outlier: 3.553A pdb=" N SER E 679 " --> pdb=" O ASP E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 699 Processing helix chain 'E' and resid 713 through 718 Processing helix chain 'E' and resid 742 through 749 removed outlier: 3.609A pdb=" N VAL E 747 " --> pdb=" O PRO E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 766 Processing helix chain 'E' and resid 770 through 792 removed outlier: 3.596A pdb=" N ASP E 782 " --> pdb=" O GLU E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 800 Processing helix chain 'F' and resid 18 through 42 removed outlier: 3.516A pdb=" N LEU F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 40 " --> pdb=" O SER F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 67 through 86 Processing helix chain 'F' and resid 98 through 109 removed outlier: 3.762A pdb=" N GLY F 102 " --> pdb=" O GLY F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 116 removed outlier: 3.607A pdb=" N GLU F 114 " --> pdb=" O GLY F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 159 through 169 removed outlier: 3.504A pdb=" N HIS F 163 " --> pdb=" O TYR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 186 Processing helix chain 'F' and resid 187 through 194 Processing helix chain 'F' and resid 195 through 199 removed outlier: 3.667A pdb=" N LYS F 198 " --> pdb=" O GLN F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 removed outlier: 3.706A pdb=" N ILE F 228 " --> pdb=" O LEU F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 240 removed outlier: 3.523A pdb=" N MET F 240 " --> pdb=" O PHE F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 284 removed outlier: 4.081A pdb=" N THR F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.689A pdb=" N SER F 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 343 removed outlier: 3.642A pdb=" N PHE F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 removed outlier: 3.828A pdb=" N LEU F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 366 through 370 removed outlier: 3.529A pdb=" N LEU F 369 " --> pdb=" O LYS F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 383 removed outlier: 4.122A pdb=" N ILE F 382 " --> pdb=" O ASN F 378 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG F 383 " --> pdb=" O GLY F 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 378 through 383' Processing helix chain 'F' and resid 390 through 394 Processing helix chain 'F' and resid 397 through 403 removed outlier: 3.769A pdb=" N GLU F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 426 removed outlier: 3.821A pdb=" N LEU F 415 " --> pdb=" O ALA F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 449 removed outlier: 3.562A pdb=" N SER F 446 " --> pdb=" O LEU F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 492 Processing helix chain 'F' and resid 504 through 507 Processing helix chain 'F' and resid 508 through 526 removed outlier: 3.529A pdb=" N ILE F 526 " --> pdb=" O THR F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.525A pdb=" N ARG F 545 " --> pdb=" O HIS F 542 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN F 546 " --> pdb=" O VAL F 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 542 through 546' Processing helix chain 'F' and resid 550 through 554 Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.524A pdb=" N VAL F 561 " --> pdb=" O GLY F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 594 Processing helix chain 'F' and resid 613 through 624 removed outlier: 4.174A pdb=" N LYS F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 665 removed outlier: 3.505A pdb=" N GLU F 664 " --> pdb=" O ASP F 660 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 665 " --> pdb=" O LYS F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 681 removed outlier: 3.553A pdb=" N SER F 679 " --> pdb=" O ASP F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 691 through 699 Processing helix chain 'F' and resid 713 through 718 Processing helix chain 'F' and resid 742 through 749 removed outlier: 3.609A pdb=" N VAL F 747 " --> pdb=" O PRO F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 766 Processing helix chain 'F' and resid 770 through 792 removed outlier: 3.596A pdb=" N ASP F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 795 through 800 Processing helix chain 'G' and resid 18 through 42 removed outlier: 3.516A pdb=" N LEU G 22 " --> pdb=" O SER G 18 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 67 through 86 Processing helix chain 'G' and resid 98 through 109 removed outlier: 3.761A pdb=" N GLY G 102 " --> pdb=" O GLY G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 116 removed outlier: 3.607A pdb=" N GLU G 114 " --> pdb=" O GLY G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 159 through 169 removed outlier: 3.504A pdb=" N HIS G 163 " --> pdb=" O TYR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 186 Processing helix chain 'G' and resid 187 through 194 Processing helix chain 'G' and resid 195 through 199 removed outlier: 3.668A pdb=" N LYS G 198 " --> pdb=" O GLN G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 removed outlier: 3.706A pdb=" N ILE G 228 " --> pdb=" O LEU G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 240 removed outlier: 3.524A pdb=" N MET G 240 " --> pdb=" O PHE G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 284 removed outlier: 4.081A pdb=" N THR G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 320 removed outlier: 3.689A pdb=" N SER G 319 " --> pdb=" O SER G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 343 removed outlier: 3.642A pdb=" N PHE G 334 " --> pdb=" O THR G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 removed outlier: 3.828A pdb=" N LEU G 349 " --> pdb=" O LYS G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 361 Processing helix chain 'G' and resid 366 through 370 removed outlier: 3.529A pdb=" N LEU G 369 " --> pdb=" O LYS G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 383 removed outlier: 4.122A pdb=" N ILE G 382 " --> pdb=" O ASN G 378 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 383 " --> pdb=" O GLY G 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 378 through 383' Processing helix chain 'G' and resid 390 through 394 Processing helix chain 'G' and resid 397 through 403 removed outlier: 3.769A pdb=" N GLU G 401 " --> pdb=" O LYS G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 426 removed outlier: 3.821A pdb=" N LEU G 415 " --> pdb=" O ALA G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 449 removed outlier: 3.562A pdb=" N SER G 446 " --> pdb=" O LEU G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 492 Processing helix chain 'G' and resid 504 through 507 Processing helix chain 'G' and resid 508 through 526 removed outlier: 3.530A pdb=" N ILE G 526 " --> pdb=" O THR G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 546 removed outlier: 3.524A pdb=" N ARG G 545 " --> pdb=" O HIS G 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN G 546 " --> pdb=" O VAL G 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 542 through 546' Processing helix chain 'G' and resid 550 through 554 Processing helix chain 'G' and resid 557 through 564 removed outlier: 3.523A pdb=" N VAL G 561 " --> pdb=" O GLY G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 594 Processing helix chain 'G' and resid 613 through 624 removed outlier: 4.174A pdb=" N LYS G 623 " --> pdb=" O ALA G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 648 through 665 removed outlier: 3.507A pdb=" N GLU G 664 " --> pdb=" O ASP G 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 665 " --> pdb=" O LYS G 661 " (cutoff:3.500A) Processing helix chain 'G' and resid 676 through 681 removed outlier: 3.553A pdb=" N SER G 679 " --> pdb=" O ASP G 676 " (cutoff:3.500A) Processing helix chain 'G' and resid 691 through 699 Processing helix chain 'G' and resid 713 through 718 Processing helix chain 'G' and resid 742 through 749 removed outlier: 3.609A pdb=" N VAL G 747 " --> pdb=" O PRO G 743 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 766 Processing helix chain 'G' and resid 770 through 792 removed outlier: 3.596A pdb=" N ASP G 782 " --> pdb=" O GLU G 778 " (cutoff:3.500A) Processing helix chain 'G' and resid 795 through 800 Processing helix chain 'H' and resid 18 through 42 removed outlier: 3.515A pdb=" N LEU H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 67 through 86 Processing helix chain 'H' and resid 98 through 109 removed outlier: 3.762A pdb=" N GLY H 102 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 116 removed outlier: 3.607A pdb=" N GLU H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 132 Processing helix chain 'H' and resid 159 through 169 removed outlier: 3.504A pdb=" N HIS H 163 " --> pdb=" O TYR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 186 Processing helix chain 'H' and resid 187 through 194 Processing helix chain 'H' and resid 195 through 199 removed outlier: 3.667A pdb=" N LYS H 198 " --> pdb=" O GLN H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 228 removed outlier: 3.706A pdb=" N ILE H 228 " --> pdb=" O LEU H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 240 removed outlier: 3.524A pdb=" N MET H 240 " --> pdb=" O PHE H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 284 removed outlier: 4.082A pdb=" N THR H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 320 removed outlier: 3.688A pdb=" N SER H 319 " --> pdb=" O SER H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 343 removed outlier: 3.642A pdb=" N PHE H 334 " --> pdb=" O THR H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 350 removed outlier: 3.829A pdb=" N LEU H 349 " --> pdb=" O LYS H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 366 through 370 removed outlier: 3.529A pdb=" N LEU H 369 " --> pdb=" O LYS H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 383 removed outlier: 4.122A pdb=" N ILE H 382 " --> pdb=" O ASN H 378 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG H 383 " --> pdb=" O GLY H 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 378 through 383' Processing helix chain 'H' and resid 390 through 394 Processing helix chain 'H' and resid 397 through 403 removed outlier: 3.769A pdb=" N GLU H 401 " --> pdb=" O LYS H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 426 removed outlier: 3.821A pdb=" N LEU H 415 " --> pdb=" O ALA H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 449 removed outlier: 3.562A pdb=" N SER H 446 " --> pdb=" O LEU H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 478 through 492 Processing helix chain 'H' and resid 504 through 507 Processing helix chain 'H' and resid 508 through 526 removed outlier: 3.529A pdb=" N ILE H 526 " --> pdb=" O THR H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 542 through 546 removed outlier: 3.525A pdb=" N ARG H 545 " --> pdb=" O HIS H 542 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN H 546 " --> pdb=" O VAL H 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 542 through 546' Processing helix chain 'H' and resid 550 through 554 Processing helix chain 'H' and resid 557 through 564 removed outlier: 3.524A pdb=" N VAL H 561 " --> pdb=" O GLY H 557 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 594 Processing helix chain 'H' and resid 613 through 624 removed outlier: 4.174A pdb=" N LYS H 623 " --> pdb=" O ALA H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 648 through 665 removed outlier: 3.506A pdb=" N GLU H 664 " --> pdb=" O ASP H 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 665 " --> pdb=" O LYS H 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 676 through 681 removed outlier: 3.553A pdb=" N SER H 679 " --> pdb=" O ASP H 676 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 699 Processing helix chain 'H' and resid 713 through 718 Processing helix chain 'H' and resid 742 through 749 removed outlier: 3.609A pdb=" N VAL H 747 " --> pdb=" O PRO H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 753 through 766 Processing helix chain 'H' and resid 770 through 792 removed outlier: 3.596A pdb=" N ASP H 782 " --> pdb=" O GLU H 778 " (cutoff:3.500A) Processing helix chain 'H' and resid 795 through 800 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN A 88 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 92 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY A 181 " --> pdb=" O ILE A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN A 88 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 174 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 209 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 176 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE A 211 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA A 178 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS A 213 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 180 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 208 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU A 294 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE A 296 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 212 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA4, first strand: chain 'A' and resid 406 through 410 removed outlier: 5.956A pdb=" N GLY A 407 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR A 610 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 474 removed outlier: 8.454A pdb=" N VAL A 474 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE A 432 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG A 431 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER A 499 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 433 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N TYR A 501 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY A 496 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU A 538 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP A 498 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER A 540 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER A 500 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY A 574 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 602 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 576 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 453 removed outlier: 5.482A pdb=" N LYS A 452 " --> pdb=" O HIS A 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 625 through 627 removed outlier: 6.293A pdb=" N VAL A 643 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA A 708 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA A 645 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N HIS A 710 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA A 647 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N TYR A 712 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR A 734 " --> pdb=" O TYR A 709 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER A 711 " --> pdb=" O TYR A 734 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.209A pdb=" N ASN B 88 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 92 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY B 181 " --> pdb=" O ILE B 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 89 removed outlier: 6.209A pdb=" N ASN B 88 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 174 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 209 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 176 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 211 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA B 178 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS B 213 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 180 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL B 208 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU B 294 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE B 296 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 212 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AB2, first strand: chain 'B' and resid 406 through 410 removed outlier: 5.957A pdb=" N GLY B 407 " --> pdb=" O THR B 610 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR B 610 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 474 removed outlier: 8.455A pdb=" N VAL B 474 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 432 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG B 431 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER B 499 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE B 433 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N TYR B 501 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY B 496 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 538 " --> pdb=" O GLY B 496 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 498 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER B 540 " --> pdb=" O TRP B 498 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER B 500 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY B 574 " --> pdb=" O ALA B 600 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE B 602 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR B 576 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 452 through 453 removed outlier: 5.482A pdb=" N LYS B 452 " --> pdb=" O HIS B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 625 through 627 removed outlier: 6.293A pdb=" N VAL B 643 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA B 708 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 645 " --> pdb=" O ALA B 708 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N HIS B 710 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA B 647 " --> pdb=" O HIS B 710 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N TYR B 712 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR B 734 " --> pdb=" O TYR B 709 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER B 711 " --> pdb=" O TYR B 734 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN C 88 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 92 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY C 181 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN C 88 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU C 174 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU C 209 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 176 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE C 211 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA C 178 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS C 213 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 180 " --> pdb=" O HIS C 213 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL C 208 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU C 294 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE C 296 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU C 212 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 406 through 410 removed outlier: 5.956A pdb=" N GLY C 407 " --> pdb=" O THR C 610 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR C 610 " --> pdb=" O GLY C 407 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 473 through 474 removed outlier: 8.455A pdb=" N VAL C 474 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE C 432 " --> pdb=" O VAL C 474 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG C 431 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER C 499 " --> pdb=" O ARG C 431 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE C 433 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N TYR C 501 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY C 496 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU C 538 " --> pdb=" O GLY C 496 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP C 498 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER C 540 " --> pdb=" O TRP C 498 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER C 500 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY C 574 " --> pdb=" O ALA C 600 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE C 602 " --> pdb=" O GLY C 574 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR C 576 " --> pdb=" O ILE C 602 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 452 through 453 removed outlier: 5.482A pdb=" N LYS C 452 " --> pdb=" O HIS C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 625 through 627 removed outlier: 6.293A pdb=" N VAL C 643 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA C 708 " --> pdb=" O VAL C 643 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 645 " --> pdb=" O ALA C 708 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N HIS C 710 " --> pdb=" O ALA C 645 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA C 647 " --> pdb=" O HIS C 710 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N TYR C 712 " --> pdb=" O ALA C 647 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR C 734 " --> pdb=" O TYR C 709 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER C 711 " --> pdb=" O TYR C 734 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN D 88 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE D 92 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY D 181 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN D 88 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU D 174 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 209 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 176 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE D 211 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA D 178 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS D 213 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL D 180 " --> pdb=" O HIS D 213 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL D 208 " --> pdb=" O PRO D 292 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU D 294 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE D 296 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU D 212 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 307 through 308 Processing sheet with id=AC7, first strand: chain 'D' and resid 406 through 410 removed outlier: 5.955A pdb=" N GLY D 407 " --> pdb=" O THR D 610 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR D 610 " --> pdb=" O GLY D 407 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 473 through 474 removed outlier: 8.455A pdb=" N VAL D 474 " --> pdb=" O PHE D 430 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE D 432 " --> pdb=" O VAL D 474 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG D 431 " --> pdb=" O ILE D 497 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER D 499 " --> pdb=" O ARG D 431 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE D 433 " --> pdb=" O SER D 499 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N TYR D 501 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY D 496 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU D 538 " --> pdb=" O GLY D 496 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP D 498 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER D 540 " --> pdb=" O TRP D 498 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER D 500 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY D 574 " --> pdb=" O ALA D 600 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE D 602 " --> pdb=" O GLY D 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR D 576 " --> pdb=" O ILE D 602 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 452 through 453 removed outlier: 5.483A pdb=" N LYS D 452 " --> pdb=" O HIS D 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 625 through 627 removed outlier: 6.293A pdb=" N VAL D 643 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA D 708 " --> pdb=" O VAL D 643 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA D 645 " --> pdb=" O ALA D 708 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N HIS D 710 " --> pdb=" O ALA D 645 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N ALA D 647 " --> pdb=" O HIS D 710 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N TYR D 712 " --> pdb=" O ALA D 647 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR D 734 " --> pdb=" O TYR D 709 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER D 711 " --> pdb=" O TYR D 734 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN E 88 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE E 92 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY E 181 " --> pdb=" O ILE E 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN E 88 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU E 174 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU E 209 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL E 176 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE E 211 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA E 178 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS E 213 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL E 180 " --> pdb=" O HIS E 213 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL E 208 " --> pdb=" O PRO E 292 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU E 294 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE E 296 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU E 212 " --> pdb=" O PHE E 296 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AD5, first strand: chain 'E' and resid 406 through 410 removed outlier: 5.956A pdb=" N GLY E 407 " --> pdb=" O THR E 610 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR E 610 " --> pdb=" O GLY E 407 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 473 through 474 removed outlier: 8.454A pdb=" N VAL E 474 " --> pdb=" O PHE E 430 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE E 432 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG E 431 " --> pdb=" O ILE E 497 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER E 499 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE E 433 " --> pdb=" O SER E 499 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N TYR E 501 " --> pdb=" O PHE E 433 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLY E 496 " --> pdb=" O ASN E 536 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU E 538 " --> pdb=" O GLY E 496 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 498 " --> pdb=" O LEU E 538 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER E 540 " --> pdb=" O TRP E 498 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER E 500 " --> pdb=" O SER E 540 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY E 574 " --> pdb=" O ALA E 600 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE E 602 " --> pdb=" O GLY E 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR E 576 " --> pdb=" O ILE E 602 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 452 through 453 removed outlier: 5.482A pdb=" N LYS E 452 " --> pdb=" O HIS E 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 625 through 627 removed outlier: 6.292A pdb=" N VAL E 643 " --> pdb=" O LEU E 706 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA E 708 " --> pdb=" O VAL E 643 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA E 645 " --> pdb=" O ALA E 708 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N HIS E 710 " --> pdb=" O ALA E 645 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA E 647 " --> pdb=" O HIS E 710 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N TYR E 712 " --> pdb=" O ALA E 647 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TYR E 734 " --> pdb=" O TYR E 709 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER E 711 " --> pdb=" O TYR E 734 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 88 through 89 removed outlier: 6.209A pdb=" N ASN F 88 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE F 92 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY F 181 " --> pdb=" O ILE F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 88 through 89 removed outlier: 6.209A pdb=" N ASN F 88 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU F 174 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU F 209 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL F 176 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 211 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA F 178 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS F 213 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL F 180 " --> pdb=" O HIS F 213 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL F 208 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU F 294 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE F 296 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU F 212 " --> pdb=" O PHE F 296 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 307 through 308 Processing sheet with id=AE3, first strand: chain 'F' and resid 406 through 410 removed outlier: 5.957A pdb=" N GLY F 407 " --> pdb=" O THR F 610 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR F 610 " --> pdb=" O GLY F 407 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 473 through 474 removed outlier: 8.454A pdb=" N VAL F 474 " --> pdb=" O PHE F 430 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE F 432 " --> pdb=" O VAL F 474 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG F 431 " --> pdb=" O ILE F 497 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER F 499 " --> pdb=" O ARG F 431 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE F 433 " --> pdb=" O SER F 499 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N TYR F 501 " --> pdb=" O PHE F 433 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY F 496 " --> pdb=" O ASN F 536 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU F 538 " --> pdb=" O GLY F 496 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP F 498 " --> pdb=" O LEU F 538 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER F 540 " --> pdb=" O TRP F 498 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER F 500 " --> pdb=" O SER F 540 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY F 574 " --> pdb=" O ALA F 600 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE F 602 " --> pdb=" O GLY F 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR F 576 " --> pdb=" O ILE F 602 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 452 through 453 removed outlier: 5.482A pdb=" N LYS F 452 " --> pdb=" O HIS F 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'F' and resid 625 through 627 removed outlier: 6.293A pdb=" N VAL F 643 " --> pdb=" O LEU F 706 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA F 708 " --> pdb=" O VAL F 643 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA F 645 " --> pdb=" O ALA F 708 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N HIS F 710 " --> pdb=" O ALA F 645 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA F 647 " --> pdb=" O HIS F 710 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N TYR F 712 " --> pdb=" O ALA F 647 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR F 734 " --> pdb=" O TYR F 709 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER F 711 " --> pdb=" O TYR F 734 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN G 88 " --> pdb=" O PHE G 175 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE G 92 " --> pdb=" O ILE G 179 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY G 181 " --> pdb=" O ILE G 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN G 88 " --> pdb=" O PHE G 175 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU G 174 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU G 209 " --> pdb=" O LEU G 174 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL G 176 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE G 211 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA G 178 " --> pdb=" O ILE G 211 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS G 213 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL G 180 " --> pdb=" O HIS G 213 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL G 208 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU G 294 " --> pdb=" O VAL G 208 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE G 296 " --> pdb=" O PRO G 210 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU G 212 " --> pdb=" O PHE G 296 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 307 through 308 Processing sheet with id=AF1, first strand: chain 'G' and resid 406 through 410 removed outlier: 5.955A pdb=" N GLY G 407 " --> pdb=" O THR G 610 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR G 610 " --> pdb=" O GLY G 407 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 473 through 474 removed outlier: 8.454A pdb=" N VAL G 474 " --> pdb=" O PHE G 430 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE G 432 " --> pdb=" O VAL G 474 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG G 431 " --> pdb=" O ILE G 497 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER G 499 " --> pdb=" O ARG G 431 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE G 433 " --> pdb=" O SER G 499 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N TYR G 501 " --> pdb=" O PHE G 433 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY G 496 " --> pdb=" O ASN G 536 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU G 538 " --> pdb=" O GLY G 496 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP G 498 " --> pdb=" O LEU G 538 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER G 540 " --> pdb=" O TRP G 498 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N SER G 500 " --> pdb=" O SER G 540 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY G 574 " --> pdb=" O ALA G 600 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE G 602 " --> pdb=" O GLY G 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR G 576 " --> pdb=" O ILE G 602 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 452 through 453 removed outlier: 5.483A pdb=" N LYS G 452 " --> pdb=" O HIS G 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'G' and resid 625 through 627 removed outlier: 6.293A pdb=" N VAL G 643 " --> pdb=" O LEU G 706 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA G 708 " --> pdb=" O VAL G 643 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA G 645 " --> pdb=" O ALA G 708 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N HIS G 710 " --> pdb=" O ALA G 645 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA G 647 " --> pdb=" O HIS G 710 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N TYR G 712 " --> pdb=" O ALA G 647 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR G 734 " --> pdb=" O TYR G 709 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER G 711 " --> pdb=" O TYR G 734 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN H 88 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE H 92 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY H 181 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'H' and resid 88 through 89 removed outlier: 6.210A pdb=" N ASN H 88 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU H 174 " --> pdb=" O ILE H 207 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU H 209 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL H 176 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE H 211 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA H 178 " --> pdb=" O ILE H 211 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS H 213 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL H 180 " --> pdb=" O HIS H 213 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL H 208 " --> pdb=" O PRO H 292 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU H 294 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE H 296 " --> pdb=" O PRO H 210 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU H 212 " --> pdb=" O PHE H 296 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 307 through 308 Processing sheet with id=AF8, first strand: chain 'H' and resid 406 through 410 removed outlier: 5.957A pdb=" N GLY H 407 " --> pdb=" O THR H 610 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR H 610 " --> pdb=" O GLY H 407 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 473 through 474 removed outlier: 8.455A pdb=" N VAL H 474 " --> pdb=" O PHE H 430 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE H 432 " --> pdb=" O VAL H 474 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG H 431 " --> pdb=" O ILE H 497 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER H 499 " --> pdb=" O ARG H 431 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE H 433 " --> pdb=" O SER H 499 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N TYR H 501 " --> pdb=" O PHE H 433 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY H 496 " --> pdb=" O ASN H 536 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU H 538 " --> pdb=" O GLY H 496 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP H 498 " --> pdb=" O LEU H 538 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER H 540 " --> pdb=" O TRP H 498 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER H 500 " --> pdb=" O SER H 540 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY H 574 " --> pdb=" O ALA H 600 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE H 602 " --> pdb=" O GLY H 574 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR H 576 " --> pdb=" O ILE H 602 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 452 through 453 removed outlier: 5.482A pdb=" N LYS H 452 " --> pdb=" O HIS H 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'H' and resid 625 through 627 removed outlier: 6.292A pdb=" N VAL H 643 " --> pdb=" O LEU H 706 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA H 708 " --> pdb=" O VAL H 643 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA H 645 " --> pdb=" O ALA H 708 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N HIS H 710 " --> pdb=" O ALA H 645 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA H 647 " --> pdb=" O HIS H 710 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N TYR H 712 " --> pdb=" O ALA H 647 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR H 734 " --> pdb=" O TYR H 709 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER H 711 " --> pdb=" O TYR H 734 " (cutoff:3.500A) 2064 hydrogen bonds defined for protein. 5712 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: 28.83 Time building geometry restraints manager: 14.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16834 1.34 - 1.45: 9167 1.45 - 1.57: 26623 1.57 - 1.69: 16 1.69 - 1.81: 280 Bond restraints: 52920 Sorted by residual: bond pdb=" O1A TPP D 900 " pdb=" PA TPP D 900 " ideal model delta sigma weight residual 1.479 1.509 -0.030 1.00e-02 1.00e+04 8.80e+00 bond pdb=" O1A TPP H 900 " pdb=" PA TPP H 900 " ideal model delta sigma weight residual 1.479 1.508 -0.029 1.00e-02 1.00e+04 8.49e+00 bond pdb=" O1A TPP F 900 " pdb=" PA TPP F 900 " ideal model delta sigma weight residual 1.479 1.508 -0.029 1.00e-02 1.00e+04 8.49e+00 bond pdb=" O1A TPP B 900 " pdb=" PA TPP B 900 " ideal model delta sigma weight residual 1.479 1.508 -0.029 1.00e-02 1.00e+04 8.13e+00 bond pdb=" O2A TPP H 900 " pdb=" PA TPP H 900 " ideal model delta sigma weight residual 1.527 1.475 0.052 2.30e-02 1.89e+03 5.05e+00 ... (remaining 52915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 69068 1.71 - 3.42: 2581 3.42 - 5.13: 279 5.13 - 6.84: 63 6.84 - 8.55: 9 Bond angle restraints: 72000 Sorted by residual: angle pdb=" O2B TPP C 900 " pdb=" PB TPP C 900 " pdb=" O3A TPP C 900 " ideal model delta sigma weight residual 104.26 110.22 -5.96 1.33e+00 5.64e-01 2.00e+01 angle pdb=" O2B TPP A 900 " pdb=" PB TPP A 900 " pdb=" O3A TPP A 900 " ideal model delta sigma weight residual 104.26 110.21 -5.95 1.33e+00 5.64e-01 1.99e+01 angle pdb=" O2B TPP G 900 " pdb=" PB TPP G 900 " pdb=" O3A TPP G 900 " ideal model delta sigma weight residual 104.26 110.20 -5.94 1.33e+00 5.64e-01 1.99e+01 angle pdb=" O2B TPP E 900 " pdb=" PB TPP E 900 " pdb=" O3A TPP E 900 " ideal model delta sigma weight residual 104.26 110.20 -5.94 1.33e+00 5.64e-01 1.99e+01 angle pdb=" N GLU A 265 " pdb=" CA GLU A 265 " pdb=" CB GLU A 265 " ideal model delta sigma weight residual 110.12 116.00 -5.88 1.47e+00 4.63e-01 1.60e+01 ... (remaining 71995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 28062 17.86 - 35.73: 2378 35.73 - 53.59: 379 53.59 - 71.46: 89 71.46 - 89.32: 68 Dihedral angle restraints: 30976 sinusoidal: 12352 harmonic: 18624 Sorted by residual: dihedral pdb=" CA VAL B 322 " pdb=" C VAL B 322 " pdb=" N PRO B 323 " pdb=" CA PRO B 323 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA VAL D 322 " pdb=" C VAL D 322 " pdb=" N PRO D 323 " pdb=" CA PRO D 323 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA VAL E 322 " pdb=" C VAL E 322 " pdb=" N PRO E 323 " pdb=" CA PRO E 323 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 30973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5757 0.055 - 0.111: 1523 0.111 - 0.166: 255 0.166 - 0.221: 9 0.221 - 0.276: 8 Chirality restraints: 7552 Sorted by residual: chirality pdb=" CA TRP A 302 " pdb=" N TRP A 302 " pdb=" C TRP A 302 " pdb=" CB TRP A 302 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA TRP F 302 " pdb=" N TRP F 302 " pdb=" C TRP F 302 " pdb=" CB TRP F 302 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA TRP E 302 " pdb=" N TRP E 302 " pdb=" C TRP E 302 " pdb=" CB TRP E 302 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 7549 not shown) Planarity restraints: 9456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 302 " 0.026 2.00e-02 2.50e+03 3.98e-02 3.96e+01 pdb=" CG TRP A 302 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP A 302 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP A 302 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 302 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 302 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 302 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 302 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 302 " 0.026 2.00e-02 2.50e+03 3.98e-02 3.96e+01 pdb=" CG TRP G 302 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP G 302 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP G 302 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 302 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP G 302 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 302 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 302 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP G 302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 302 " 0.026 2.00e-02 2.50e+03 3.97e-02 3.95e+01 pdb=" CG TRP E 302 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP E 302 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP E 302 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 302 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP E 302 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 302 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 302 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP E 302 " -0.001 2.00e-02 2.50e+03 ... (remaining 9453 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 358 2.50 - 3.10: 37738 3.10 - 3.70: 83807 3.70 - 4.30: 129985 4.30 - 4.90: 213517 Nonbonded interactions: 465405 Sorted by model distance: nonbonded pdb=" O1B TPP H 900 " pdb="MG MG H 901 " model vdw 1.898 2.170 nonbonded pdb=" O2B TPP G 900 " pdb="MG MG G 901 " model vdw 1.898 2.170 nonbonded pdb=" O2B TPP C 900 " pdb="MG MG C 901 " model vdw 1.898 2.170 nonbonded pdb=" O2B TPP E 900 " pdb="MG MG E 901 " model vdw 1.898 2.170 nonbonded pdb=" O1B TPP F 900 " pdb="MG MG F 901 " model vdw 1.898 2.170 ... (remaining 465400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.820 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 115.600 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 52920 Z= 0.464 Angle : 0.758 8.547 72000 Z= 0.450 Chirality : 0.049 0.276 7552 Planarity : 0.005 0.050 9456 Dihedral : 14.097 89.320 19056 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 6432 helix: -0.17 (0.09), residues: 2592 sheet: -0.52 (0.19), residues: 824 loop : -0.64 (0.11), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP A 302 HIS 0.012 0.002 HIS H 213 PHE 0.030 0.003 PHE C 143 TYR 0.028 0.002 TYR G 402 ARG 0.007 0.001 ARG E 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 5.889 Fit side-chains outliers start: 0 outliers final: 8 residues processed: 580 average time/residue: 1.5638 time to fit residues: 1155.5753 Evaluate side-chains 310 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 302 time to evaluate : 5.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain E residue 782 ASP Chi-restraints excluded: chain F residue 782 ASP Chi-restraints excluded: chain G residue 782 ASP Chi-restraints excluded: chain H residue 782 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 20.0000 chunk 485 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 259 optimal weight: 0.9980 chunk 501 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 305 optimal weight: 9.9990 chunk 373 optimal weight: 2.9990 chunk 581 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS A 568 HIS ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 568 HIS ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 HIS ** D 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS E 568 HIS ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 HIS F 568 HIS ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 HIS G 568 HIS ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 568 HIS ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 52920 Z= 0.190 Angle : 0.570 10.265 72000 Z= 0.308 Chirality : 0.043 0.159 7552 Planarity : 0.005 0.047 9456 Dihedral : 6.566 78.470 7064 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.33 % Allowed : 4.91 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 6432 helix: 0.91 (0.10), residues: 2624 sheet: -0.34 (0.19), residues: 832 loop : -0.29 (0.12), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 302 HIS 0.008 0.001 HIS B 320 PHE 0.013 0.001 PHE D 143 TYR 0.012 0.001 TYR B 165 ARG 0.006 0.000 ARG H 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 384 time to evaluate : 5.804 Fit side-chains REVERT: A 715 ASP cc_start: 0.6118 (m-30) cc_final: 0.5909 (m-30) REVERT: F 715 ASP cc_start: 0.6141 (m-30) cc_final: 0.5931 (m-30) outliers start: 72 outliers final: 0 residues processed: 423 average time/residue: 1.4037 time to fit residues: 774.6173 Evaluate side-chains 316 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 483 optimal weight: 8.9990 chunk 395 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 582 optimal weight: 3.9990 chunk 628 optimal weight: 8.9990 chunk 518 optimal weight: 8.9990 chunk 577 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 467 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 468 HIS ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 468 HIS ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.086 52920 Z= 0.629 Angle : 0.711 8.093 72000 Z= 0.375 Chirality : 0.050 0.167 7552 Planarity : 0.005 0.048 9456 Dihedral : 6.339 83.804 7048 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.17 % Allowed : 7.31 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 6432 helix: 1.07 (0.10), residues: 2568 sheet: -0.02 (0.21), residues: 768 loop : -0.33 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 302 HIS 0.009 0.002 HIS A 213 PHE 0.016 0.002 PHE D 73 TYR 0.012 0.002 TYR C 709 ARG 0.004 0.001 ARG E 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 302 time to evaluate : 5.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 33 residues processed: 373 average time/residue: 1.5580 time to fit residues: 743.3626 Evaluate side-chains 320 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 511 MET Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 622 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 461 ASP Chi-restraints excluded: chain F residue 622 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 622 GLU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 511 MET Chi-restraints excluded: chain H residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 3.9990 chunk 437 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 390 optimal weight: 3.9990 chunk 584 optimal weight: 0.8980 chunk 618 optimal weight: 1.9990 chunk 305 optimal weight: 9.9990 chunk 553 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 52920 Z= 0.227 Angle : 0.532 6.515 72000 Z= 0.284 Chirality : 0.043 0.156 7552 Planarity : 0.004 0.046 9456 Dihedral : 6.032 83.273 7048 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.28 % Allowed : 9.89 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 6432 helix: 1.39 (0.10), residues: 2600 sheet: -0.37 (0.20), residues: 840 loop : -0.14 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 302 HIS 0.008 0.001 HIS G 506 PHE 0.011 0.001 PHE A 263 TYR 0.013 0.001 TYR B 165 ARG 0.004 0.000 ARG G 751 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 354 time to evaluate : 5.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 24 residues processed: 410 average time/residue: 1.4876 time to fit residues: 788.7717 Evaluate side-chains 342 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 318 time to evaluate : 5.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 622 GLU Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 622 GLU Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 622 GLU Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 412 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 0.9990 chunk 351 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 460 optimal weight: 8.9990 chunk 255 optimal weight: 8.9990 chunk 527 optimal weight: 2.9990 chunk 427 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 555 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 52920 Z= 0.357 Angle : 0.570 7.201 72000 Z= 0.301 Chirality : 0.044 0.162 7552 Planarity : 0.004 0.046 9456 Dihedral : 5.978 87.361 7048 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.41 % Allowed : 10.61 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.11), residues: 6432 helix: 1.55 (0.10), residues: 2560 sheet: -0.41 (0.20), residues: 840 loop : -0.04 (0.12), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 302 HIS 0.006 0.001 HIS H 506 PHE 0.011 0.001 PHE A 263 TYR 0.009 0.001 TYR B 165 ARG 0.003 0.000 ARG H 618 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 305 time to evaluate : 5.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 35 residues processed: 361 average time/residue: 1.5503 time to fit residues: 719.1994 Evaluate side-chains 336 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 5.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 511 MET Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 461 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 412 THR Chi-restraints excluded: chain H residue 511 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 6.9990 chunk 557 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 363 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 619 optimal weight: 0.9980 chunk 514 optimal weight: 0.0270 chunk 286 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 325 optimal weight: 1.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 52920 Z= 0.262 Angle : 0.549 8.186 72000 Z= 0.289 Chirality : 0.043 0.160 7552 Planarity : 0.004 0.046 9456 Dihedral : 5.894 89.865 7048 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.22 % Allowed : 11.09 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.11), residues: 6432 helix: 1.60 (0.10), residues: 2552 sheet: -0.53 (0.20), residues: 856 loop : -0.00 (0.12), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 302 HIS 0.005 0.001 HIS E 506 PHE 0.011 0.001 PHE A 263 TYR 0.011 0.001 TYR B 165 ARG 0.003 0.000 ARG G 751 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 327 time to evaluate : 6.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 28 residues processed: 375 average time/residue: 1.4997 time to fit residues: 729.6799 Evaluate side-chains 332 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 511 MET Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 511 MET Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 461 ASP Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 412 THR Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 511 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 0.0170 chunk 69 optimal weight: 7.9990 chunk 352 optimal weight: 0.6980 chunk 452 optimal weight: 0.9990 chunk 350 optimal weight: 0.4980 chunk 521 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 616 optimal weight: 6.9990 chunk 386 optimal weight: 1.9990 chunk 376 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS B 142 HIS C 142 HIS D 142 HIS E 142 HIS G 142 HIS ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 52920 Z= 0.161 Angle : 0.513 8.948 72000 Z= 0.271 Chirality : 0.042 0.151 7552 Planarity : 0.004 0.045 9456 Dihedral : 5.610 85.523 7048 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.76 % Allowed : 12.26 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.11), residues: 6432 helix: 1.65 (0.10), residues: 2592 sheet: -0.59 (0.19), residues: 864 loop : 0.08 (0.12), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 302 HIS 0.007 0.001 HIS G 480 PHE 0.009 0.001 PHE A 263 TYR 0.014 0.001 TYR C 165 ARG 0.003 0.000 ARG G 751 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 372 time to evaluate : 5.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 10 residues processed: 406 average time/residue: 1.5750 time to fit residues: 817.2407 Evaluate side-chains 333 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 323 time to evaluate : 5.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 498 TRP Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 498 TRP Chi-restraints excluded: chain H residue 322 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 368 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 392 optimal weight: 7.9990 chunk 420 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 484 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS C 59 HIS D 59 HIS E 59 HIS F 59 HIS G 59 HIS ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 HIS ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 52920 Z= 0.254 Angle : 0.545 9.839 72000 Z= 0.284 Chirality : 0.043 0.157 7552 Planarity : 0.004 0.045 9456 Dihedral : 5.557 83.300 7048 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.48 % Allowed : 13.20 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.11), residues: 6432 helix: 1.68 (0.10), residues: 2600 sheet: -0.58 (0.19), residues: 872 loop : 0.13 (0.12), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 302 HIS 0.004 0.001 HIS F 77 PHE 0.010 0.001 PHE A 263 TYR 0.010 0.001 TYR A 165 ARG 0.003 0.000 ARG C 751 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 5.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 334 average time/residue: 1.6219 time to fit residues: 689.3351 Evaluate side-chains 323 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 312 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 461 ASP Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain H residue 322 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 10.0000 chunk 590 optimal weight: 7.9990 chunk 539 optimal weight: 3.9990 chunk 574 optimal weight: 0.0370 chunk 345 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 451 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 519 optimal weight: 0.9980 chunk 543 optimal weight: 9.9990 chunk 572 optimal weight: 0.7980 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 52920 Z= 0.235 Angle : 0.548 10.349 72000 Z= 0.286 Chirality : 0.042 0.164 7552 Planarity : 0.004 0.044 9456 Dihedral : 5.511 82.446 7048 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.70 % Allowed : 13.00 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.11), residues: 6432 helix: 1.78 (0.10), residues: 2552 sheet: -0.57 (0.19), residues: 872 loop : 0.15 (0.12), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 302 HIS 0.004 0.001 HIS B 77 PHE 0.009 0.001 PHE H 263 TYR 0.010 0.001 TYR H 165 ARG 0.003 0.000 ARG D 751 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 324 time to evaluate : 5.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 354 average time/residue: 1.6284 time to fit residues: 732.5551 Evaluate side-chains 338 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 315 time to evaluate : 6.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 555 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 555 ASP Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 461 ASP Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 422 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 9.9990 chunk 607 optimal weight: 10.0000 chunk 371 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 422 optimal weight: 0.3980 chunk 637 optimal weight: 4.9990 chunk 586 optimal weight: 0.8980 chunk 507 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 392 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 52920 Z= 0.180 Angle : 0.557 10.885 72000 Z= 0.288 Chirality : 0.042 0.154 7552 Planarity : 0.004 0.045 9456 Dihedral : 5.453 84.055 7048 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.43 % Allowed : 13.56 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.11), residues: 6432 helix: 1.80 (0.10), residues: 2552 sheet: -0.57 (0.19), residues: 888 loop : 0.17 (0.12), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 302 HIS 0.004 0.001 HIS B 77 PHE 0.009 0.001 PHE B 263 TYR 0.012 0.001 TYR H 165 ARG 0.004 0.000 ARG F 751 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 348 time to evaluate : 5.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 27 residues processed: 371 average time/residue: 1.5759 time to fit residues: 748.5369 Evaluate side-chains 351 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 5.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 498 TRP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 498 TRP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 498 TRP Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 498 TRP Chi-restraints excluded: chain D residue 555 ASP Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 498 TRP Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 555 ASP Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 555 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 498 TRP Chi-restraints excluded: chain H residue 555 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 5.9990 chunk 540 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 468 optimal weight: 8.9990 chunk 74 optimal weight: 0.0370 chunk 141 optimal weight: 9.9990 chunk 508 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 522 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 93 optimal weight: 0.0570 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079568 restraints weight = 114505.493| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.88 r_work: 0.3125 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52920 Z= 0.176 Angle : 0.547 11.624 72000 Z= 0.283 Chirality : 0.042 0.204 7552 Planarity : 0.004 0.066 9456 Dihedral : 5.405 85.283 7048 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.43 % Allowed : 13.87 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.11), residues: 6432 helix: 1.83 (0.10), residues: 2552 sheet: -0.53 (0.19), residues: 888 loop : 0.19 (0.12), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 498 HIS 0.004 0.001 HIS B 77 PHE 0.009 0.001 PHE C 263 TYR 0.012 0.001 TYR B 165 ARG 0.004 0.000 ARG B 751 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13489.78 seconds wall clock time: 244 minutes 32.53 seconds (14672.53 seconds total)