Starting phenix.real_space_refine on Tue Apr 16 19:16:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqi_35671/04_2024/8iqi_35671_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqi_35671/04_2024/8iqi_35671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqi_35671/04_2024/8iqi_35671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqi_35671/04_2024/8iqi_35671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqi_35671/04_2024/8iqi_35671_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqi_35671/04_2024/8iqi_35671_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 25 5.49 5 Mg 4 5.21 5 S 139 5.16 5 C 25602 2.51 5 N 7134 2.21 5 O 7528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 624": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A ARG 704": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ARG 752": "NH1" <-> "NH2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A ARG 757": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ARG 829": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "A ARG 901": "NH1" <-> "NH2" Residue "A ARG 907": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 513": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 624": "NH1" <-> "NH2" Residue "B ARG 647": "NH1" <-> "NH2" Residue "B ARG 670": "NH1" <-> "NH2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B ARG 686": "NH1" <-> "NH2" Residue "B ARG 704": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 751": "NH1" <-> "NH2" Residue "B ARG 752": "NH1" <-> "NH2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "B ARG 779": "NH1" <-> "NH2" Residue "B ARG 829": "NH1" <-> "NH2" Residue "B ARG 842": "NH1" <-> "NH2" Residue "B ARG 874": "NH1" <-> "NH2" Residue "B ARG 901": "NH1" <-> "NH2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C ARG 376": "NH1" <-> "NH2" Residue "C ARG 461": "NH1" <-> "NH2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C ARG 513": "NH1" <-> "NH2" Residue "C PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 536": "NH1" <-> "NH2" Residue "C ARG 538": "NH1" <-> "NH2" Residue "C ARG 611": "NH1" <-> "NH2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C ARG 670": "NH1" <-> "NH2" Residue "C ARG 682": "NH1" <-> "NH2" Residue "C ARG 686": "NH1" <-> "NH2" Residue "C ARG 704": "NH1" <-> "NH2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 751": "NH1" <-> "NH2" Residue "C ARG 752": "NH1" <-> "NH2" Residue "C ARG 754": "NH1" <-> "NH2" Residue "C ARG 757": "NH1" <-> "NH2" Residue "C ARG 779": "NH1" <-> "NH2" Residue "C ARG 829": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C ARG 874": "NH1" <-> "NH2" Residue "C ARG 907": "NH1" <-> "NH2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ARG 461": "NH1" <-> "NH2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D ARG 513": "NH1" <-> "NH2" Residue "D ARG 529": "NH1" <-> "NH2" Residue "D ARG 536": "NH1" <-> "NH2" Residue "D ARG 538": "NH1" <-> "NH2" Residue "D ARG 611": "NH1" <-> "NH2" Residue "D ARG 624": "NH1" <-> "NH2" Residue "D ARG 647": "NH1" <-> "NH2" Residue "D ARG 670": "NH1" <-> "NH2" Residue "D ARG 682": "NH1" <-> "NH2" Residue "D ARG 686": "NH1" <-> "NH2" Residue "D ARG 704": "NH1" <-> "NH2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D ARG 751": "NH1" <-> "NH2" Residue "D ARG 752": "NH1" <-> "NH2" Residue "D ARG 754": "NH1" <-> "NH2" Residue "D ARG 757": "NH1" <-> "NH2" Residue "D ARG 779": "NH1" <-> "NH2" Residue "D ARG 829": "NH1" <-> "NH2" Residue "D ARG 837": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 874": "NH1" <-> "NH2" Residue "D ARG 901": "NH1" <-> "NH2" Residue "D ARG 907": "NH1" <-> "NH2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E ARG 376": "NH1" <-> "NH2" Residue "E ARG 461": "NH1" <-> "NH2" Residue "E ARG 479": "NH1" <-> "NH2" Residue "E ARG 483": "NH1" <-> "NH2" Residue "E ARG 513": "NH1" <-> "NH2" Residue "E ARG 529": "NH1" <-> "NH2" Residue "E ARG 536": "NH1" <-> "NH2" Residue "E ARG 538": "NH1" <-> "NH2" Residue "E ARG 611": "NH1" <-> "NH2" Residue "E ARG 624": "NH1" <-> "NH2" Residue "E ARG 647": "NH1" <-> "NH2" Residue "E ARG 670": "NH1" <-> "NH2" Residue "E ARG 682": "NH1" <-> "NH2" Residue "E ARG 686": "NH1" <-> "NH2" Residue "E ARG 704": "NH1" <-> "NH2" Residue "E ARG 717": "NH1" <-> "NH2" Residue "E ARG 751": "NH1" <-> "NH2" Residue "E ARG 752": "NH1" <-> "NH2" Residue "E ARG 754": "NH1" <-> "NH2" Residue "E ARG 757": "NH1" <-> "NH2" Residue "E ARG 779": "NH1" <-> "NH2" Residue "E ARG 829": "NH1" <-> "NH2" Residue "E ARG 837": "NH1" <-> "NH2" Residue "E ARG 874": "NH1" <-> "NH2" Residue "E ARG 901": "NH1" <-> "NH2" Residue "E ARG 907": "NH1" <-> "NH2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 367": "NH1" <-> "NH2" Residue "F ARG 376": "NH1" <-> "NH2" Residue "F ARG 461": "NH1" <-> "NH2" Residue "F ARG 479": "NH1" <-> "NH2" Residue "F ARG 483": "NH1" <-> "NH2" Residue "F ARG 513": "NH1" <-> "NH2" Residue "F PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 529": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ARG 538": "NH1" <-> "NH2" Residue "F ARG 611": "NH1" <-> "NH2" Residue "F ARG 624": "NH1" <-> "NH2" Residue "F ARG 647": "NH1" <-> "NH2" Residue "F ARG 670": "NH1" <-> "NH2" Residue "F ARG 682": "NH1" <-> "NH2" Residue "F ARG 686": "NH1" <-> "NH2" Residue "F PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 704": "NH1" <-> "NH2" Residue "F ARG 751": "NH1" <-> "NH2" Residue "F ARG 752": "NH1" <-> "NH2" Residue "F ARG 754": "NH1" <-> "NH2" Residue "F ARG 757": "NH1" <-> "NH2" Residue "F ARG 779": "NH1" <-> "NH2" Residue "F ARG 829": "NH1" <-> "NH2" Residue "F ARG 837": "NH1" <-> "NH2" Residue "F ARG 842": "NH1" <-> "NH2" Residue "F ARG 874": "NH1" <-> "NH2" Residue "F ARG 901": "NH1" <-> "NH2" Residue "F ARG 907": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40432 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 6625 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 869} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 935 Unresolved non-hydrogen angles: 1194 Unresolved non-hydrogen dihedrals: 775 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 13, 'TYR:plan': 13, 'ASN:plan1': 11, 'ASP:plan': 9, 'PHE:plan': 10, 'GLU:plan': 23, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 484 Chain: "B" Number of atoms: 6699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 6699 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 242} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 870} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 857 Unresolved non-hydrogen angles: 1094 Unresolved non-hydrogen dihedrals: 713 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 12, 'TYR:plan': 12, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 10, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 445 Chain: "C" Number of atoms: 6699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 6699 Classifications: {'peptide': 916} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 871} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 865 Unresolved non-hydrogen angles: 1106 Unresolved non-hydrogen dihedrals: 717 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 12, 'TYR:plan': 12, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 10, 'GLU:plan': 18, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 445 Chain: "D" Number of atoms: 6720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 6720 Classifications: {'peptide': 916} Incomplete info: {'truncation_to_alanine': 240} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 871} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 844 Unresolved non-hydrogen angles: 1079 Unresolved non-hydrogen dihedrals: 702 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 12, 'TYR:plan': 12, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 10, 'GLU:plan': 18, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 435 Chain: "E" Number of atoms: 6664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 6664 Classifications: {'peptide': 916} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 871} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 901 Unresolved non-hydrogen angles: 1153 Unresolved non-hydrogen dihedrals: 745 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 12, 'TYR:plan': 13, 'ASN:plan1': 12, 'ASP:plan': 9, 'PHE:plan': 10, 'GLU:plan': 20, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 466 Chain: "F" Number of atoms: 6647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6647 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 246} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 865} Chain breaks: 3 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 870 Unresolved non-hydrogen angles: 1111 Unresolved non-hydrogen dihedrals: 724 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 12, 'TYR:plan': 12, 'ASN:plan1': 11, 'ASP:plan': 10, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 456 Chain: "G" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ANP%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 10 Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.16, per 1000 atoms: 0.55 Number of scatterers: 40432 At special positions: 0 Unit cell: (196.9, 190.3, 190.3, 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 139 16.00 P 25 15.00 Mg 4 11.99 O 7528 8.00 N 7134 7.00 C 25602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.02 Conformation dependent library (CDL) restraints added in 7.9 seconds 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 237 helices and 51 sheets defined 45.4% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.63 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 112 through 129 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 201 through 204 removed outlier: 4.227A pdb=" N ALA A 204 " --> pdb=" O PRO A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 204' Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 285 through 296 removed outlier: 3.903A pdb=" N LEU A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.671A pdb=" N ASN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 336 through 345 removed outlier: 3.745A pdb=" N LYS A 345 " --> pdb=" O TRP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 354 through 367 Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 387 through 408 removed outlier: 3.636A pdb=" N GLU A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 426 Processing helix chain 'A' and resid 467 through 475 removed outlier: 3.651A pdb=" N SER A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 498 through 519 removed outlier: 4.199A pdb=" N SER A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 4.455A pdb=" N PHE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 604 Processing helix chain 'A' and resid 608 through 621 removed outlier: 3.506A pdb=" N THR A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 657 removed outlier: 3.618A pdb=" N MET A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP A 655 " --> pdb=" O MET A 651 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N HIS A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 678 through 683 removed outlier: 4.211A pdb=" N LEU A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 747 through 752 removed outlier: 4.022A pdb=" N ARG A 752 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 782 Processing helix chain 'A' and resid 788 through 809 Processing helix chain 'A' and resid 813 through 815 No H-bonds generated for 'chain 'A' and resid 813 through 815' Processing helix chain 'A' and resid 819 through 830 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 847 through 849 No H-bonds generated for 'chain 'A' and resid 847 through 849' Processing helix chain 'A' and resid 855 through 869 Processing helix chain 'A' and resid 877 through 886 Processing helix chain 'A' and resid 888 through 891 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'B' and resid 10 through 20 removed outlier: 4.163A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 33 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 62 through 77 Processing helix chain 'B' and resid 112 through 129 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 181 through 190 removed outlier: 3.752A pdb=" N GLN B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 204 removed outlier: 4.410A pdb=" N ALA B 204 " --> pdb=" O PRO B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 204' Processing helix chain 'B' and resid 252 through 255 No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.539A pdb=" N HIS B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 removed outlier: 3.561A pdb=" N ASN B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 336 through 345 removed outlier: 3.704A pdb=" N LYS B 345 " --> pdb=" O TRP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 354 through 367 removed outlier: 3.569A pdb=" N SER B 366 " --> pdb=" O TRP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 387 through 408 Processing helix chain 'B' and resid 415 through 426 Processing helix chain 'B' and resid 467 through 475 removed outlier: 3.711A pdb=" N SER B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 493 removed outlier: 3.643A pdb=" N MET B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 519 removed outlier: 4.193A pdb=" N SER B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS B 517 " --> pdb=" O ARG B 513 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 534 removed outlier: 4.568A pdb=" N PHE B 533 " --> pdb=" O ARG B 529 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 604 Processing helix chain 'B' and resid 608 through 621 removed outlier: 3.565A pdb=" N THR B 620 " --> pdb=" O PHE B 616 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 653 removed outlier: 3.552A pdb=" N ALA B 650 " --> pdb=" O MET B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.765A pdb=" N THR B 667 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 removed outlier: 4.479A pdb=" N LEU B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 708 Processing helix chain 'B' and resid 747 through 750 No H-bonds generated for 'chain 'B' and resid 747 through 750' Processing helix chain 'B' and resid 778 through 782 removed outlier: 3.660A pdb=" N HIS B 782 " --> pdb=" O ARG B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 788 through 809 Processing helix chain 'B' and resid 813 through 815 No H-bonds generated for 'chain 'B' and resid 813 through 815' Processing helix chain 'B' and resid 819 through 832 Processing helix chain 'B' and resid 834 through 842 Processing helix chain 'B' and resid 855 through 869 Processing helix chain 'B' and resid 877 through 886 removed outlier: 3.604A pdb=" N ASN B 886 " --> pdb=" O GLN B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 35 through 38 Processing helix chain 'C' and resid 62 through 77 removed outlier: 3.538A pdb=" N GLN C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 181 through 189 Processing helix chain 'C' and resid 201 through 204 removed outlier: 3.514A pdb=" N ALA C 204 " --> pdb=" O PRO C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 298 through 309 removed outlier: 3.548A pdb=" N LYS C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 331 Processing helix chain 'C' and resid 336 through 345 removed outlier: 3.528A pdb=" N LYS C 345 " --> pdb=" O TRP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 387 through 409 Processing helix chain 'C' and resid 415 through 426 Processing helix chain 'C' and resid 467 through 475 removed outlier: 3.617A pdb=" N SER C 474 " --> pdb=" O HIS C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 498 through 519 removed outlier: 4.264A pdb=" N SER C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 534 removed outlier: 4.300A pdb=" N PHE C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 604 Processing helix chain 'C' and resid 608 through 621 removed outlier: 3.610A pdb=" N THR C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA C 621 " --> pdb=" O TYR C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 657 removed outlier: 3.560A pdb=" N ALA C 650 " --> pdb=" O MET C 646 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASP C 655 " --> pdb=" O MET C 651 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N HIS C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 667 removed outlier: 3.765A pdb=" N THR C 667 " --> pdb=" O SER C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 683 removed outlier: 4.332A pdb=" N LEU C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 708 removed outlier: 3.520A pdb=" N GLU C 707 " --> pdb=" O SER C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 750 No H-bonds generated for 'chain 'C' and resid 747 through 750' Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 788 through 809 Processing helix chain 'C' and resid 813 through 815 No H-bonds generated for 'chain 'C' and resid 813 through 815' Processing helix chain 'C' and resid 819 through 832 Processing helix chain 'C' and resid 834 through 842 Processing helix chain 'C' and resid 855 through 869 Processing helix chain 'C' and resid 877 through 885 Processing helix chain 'C' and resid 888 through 890 No H-bonds generated for 'chain 'C' and resid 888 through 890' Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 35 through 38 Processing helix chain 'D' and resid 62 through 78 removed outlier: 3.868A pdb=" N GLN D 78 " --> pdb=" O GLN D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 181 through 189 Processing helix chain 'D' and resid 201 through 204 removed outlier: 4.439A pdb=" N ALA D 204 " --> pdb=" O PRO D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 201 through 204' Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 298 through 309 removed outlier: 4.225A pdb=" N LEU D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.733A pdb=" N VAL D 316 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 336 through 345 removed outlier: 3.559A pdb=" N LYS D 345 " --> pdb=" O TRP D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 354 through 367 Processing helix chain 'D' and resid 375 through 385 Processing helix chain 'D' and resid 387 through 409 Processing helix chain 'D' and resid 415 through 425 removed outlier: 3.723A pdb=" N VAL D 421 " --> pdb=" O MET D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 475 removed outlier: 3.601A pdb=" N SER D 474 " --> pdb=" O HIS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 493 removed outlier: 3.564A pdb=" N MET D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 519 removed outlier: 4.158A pdb=" N SER D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS D 517 " --> pdb=" O ARG D 513 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE D 518 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N PHE D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 534 removed outlier: 4.442A pdb=" N PHE D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 604 Processing helix chain 'D' and resid 608 through 621 removed outlier: 3.596A pdb=" N THR D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA D 621 " --> pdb=" O TYR D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 657 removed outlier: 3.562A pdb=" N VAL D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 650 " --> pdb=" O MET D 646 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASP D 655 " --> pdb=" O MET D 651 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N HIS D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 666 Processing helix chain 'D' and resid 678 through 683 removed outlier: 4.777A pdb=" N LEU D 683 " --> pdb=" O ALA D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 708 Processing helix chain 'D' and resid 747 through 752 removed outlier: 4.724A pdb=" N ARG D 752 " --> pdb=" O GLY D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 782 removed outlier: 3.558A pdb=" N HIS D 782 " --> pdb=" O ARG D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 808 Processing helix chain 'D' and resid 813 through 815 No H-bonds generated for 'chain 'D' and resid 813 through 815' Processing helix chain 'D' and resid 819 through 832 Processing helix chain 'D' and resid 834 through 842 Processing helix chain 'D' and resid 855 through 869 Processing helix chain 'D' and resid 877 through 886 removed outlier: 3.699A pdb=" N GLN D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 890 through 892 No H-bonds generated for 'chain 'D' and resid 890 through 892' Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 22 through 33 Processing helix chain 'E' and resid 35 through 38 Processing helix chain 'E' and resid 62 through 77 Processing helix chain 'E' and resid 112 through 129 Processing helix chain 'E' and resid 167 through 179 Processing helix chain 'E' and resid 181 through 189 Processing helix chain 'E' and resid 201 through 204 removed outlier: 3.615A pdb=" N ALA E 204 " --> pdb=" O PRO E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 201 through 204' Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 298 through 309 removed outlier: 4.111A pdb=" N LEU E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.909A pdb=" N VAL E 316 " --> pdb=" O GLU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 331 Processing helix chain 'E' and resid 335 through 344 Processing helix chain 'E' and resid 347 through 351 Processing helix chain 'E' and resid 354 through 366 removed outlier: 4.162A pdb=" N SER E 366 " --> pdb=" O TRP E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 385 Processing helix chain 'E' and resid 387 through 408 removed outlier: 3.580A pdb=" N TYR E 405 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 426 Processing helix chain 'E' and resid 467 through 493 removed outlier: 3.586A pdb=" N SER E 474 " --> pdb=" O HIS E 470 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE E 477 " --> pdb=" O ILE E 473 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER E 478 " --> pdb=" O SER E 474 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG E 479 " --> pdb=" O GLU E 475 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 519 removed outlier: 4.095A pdb=" N SER E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LYS E 517 " --> pdb=" O ARG E 513 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE E 518 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE E 519 " --> pdb=" O LYS E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 533 removed outlier: 4.404A pdb=" N PHE E 533 " --> pdb=" O ARG E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 604 Processing helix chain 'E' and resid 608 through 621 removed outlier: 3.634A pdb=" N THR E 620 " --> pdb=" O PHE E 616 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA E 621 " --> pdb=" O TYR E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 653 Processing helix chain 'E' and resid 663 through 667 Processing helix chain 'E' and resid 678 through 683 removed outlier: 4.490A pdb=" N LEU E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 708 Processing helix chain 'E' and resid 747 through 752 removed outlier: 4.701A pdb=" N ARG E 752 " --> pdb=" O GLY E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 778 through 782 removed outlier: 3.624A pdb=" N HIS E 782 " --> pdb=" O ARG E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 809 Processing helix chain 'E' and resid 813 through 815 No H-bonds generated for 'chain 'E' and resid 813 through 815' Processing helix chain 'E' and resid 819 through 831 Processing helix chain 'E' and resid 834 through 841 Processing helix chain 'E' and resid 855 through 869 Processing helix chain 'E' and resid 877 through 886 Processing helix chain 'E' and resid 888 through 891 removed outlier: 4.243A pdb=" N LYS E 891 " --> pdb=" O VAL E 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 888 through 891' Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'F' and resid 10 through 20 removed outlier: 3.525A pdb=" N ARG F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS F 19 " --> pdb=" O THR F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 33 Processing helix chain 'F' and resid 35 through 38 Processing helix chain 'F' and resid 62 through 77 Processing helix chain 'F' and resid 112 through 128 Processing helix chain 'F' and resid 167 through 179 Processing helix chain 'F' and resid 181 through 190 Processing helix chain 'F' and resid 201 through 204 removed outlier: 3.852A pdb=" N ALA F 204 " --> pdb=" O PRO F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 204' Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 252 through 255 No H-bonds generated for 'chain 'F' and resid 252 through 255' Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 298 through 309 removed outlier: 4.253A pdb=" N LEU F 309 " --> pdb=" O LYS F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 331 Processing helix chain 'F' and resid 336 through 345 Processing helix chain 'F' and resid 347 through 351 Processing helix chain 'F' and resid 354 through 365 Processing helix chain 'F' and resid 375 through 385 Processing helix chain 'F' and resid 387 through 408 removed outlier: 3.613A pdb=" N TYR F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 426 Processing helix chain 'F' and resid 467 through 475 removed outlier: 3.708A pdb=" N SER F 474 " --> pdb=" O HIS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 493 Processing helix chain 'F' and resid 498 through 519 removed outlier: 4.146A pdb=" N SER F 516 " --> pdb=" O GLU F 512 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS F 517 " --> pdb=" O ARG F 513 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE F 518 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE F 519 " --> pdb=" O LYS F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 534 removed outlier: 4.478A pdb=" N PHE F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU F 534 " --> pdb=" O GLN F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 543 No H-bonds generated for 'chain 'F' and resid 541 through 543' Processing helix chain 'F' and resid 592 through 604 Processing helix chain 'F' and resid 608 through 621 removed outlier: 3.651A pdb=" N THR F 620 " --> pdb=" O PHE F 616 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA F 621 " --> pdb=" O TYR F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 653 Processing helix chain 'F' and resid 663 through 667 removed outlier: 3.509A pdb=" N THR F 667 " --> pdb=" O SER F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 682 No H-bonds generated for 'chain 'F' and resid 680 through 682' Processing helix chain 'F' and resid 702 through 706 Processing helix chain 'F' and resid 747 through 752 removed outlier: 4.323A pdb=" N ARG F 752 " --> pdb=" O GLY F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 778 through 786 removed outlier: 4.735A pdb=" N ILE F 785 " --> pdb=" O ILE F 781 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N MET F 786 " --> pdb=" O HIS F 782 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 809 Processing helix chain 'F' and resid 819 through 831 Processing helix chain 'F' and resid 834 through 841 Processing helix chain 'F' and resid 855 through 869 Processing helix chain 'F' and resid 877 through 884 Processing helix chain 'F' and resid 888 through 892 removed outlier: 3.571A pdb=" N LYS F 891 " --> pdb=" O VAL F 888 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 56 through 58 Processing sheet with id= B, first strand: chain 'A' and resid 91 through 101 removed outlier: 6.544A pdb=" N LEU A 163 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 11.240A pdb=" N LEU A 96 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 11.420A pdb=" N TYR A 98 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N LEU A 159 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N LEU A 100 " --> pdb=" O HIS A 157 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N HIS A 157 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N HIS A 140 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 163 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 11.646A pdb=" N LYS A 138 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 15.901A pdb=" N MET A 165 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 19.560A pdb=" N SER A 136 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 225 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 145 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A 223 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 226 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.818A pdb=" N TRP A 442 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.626A pdb=" N GLY A 556 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 753 through 757 removed outlier: 6.301A pdb=" N MET A 631 " --> pdb=" O ARG A 754 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR A 756 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 633 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET A 732 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TRP A 634 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 734 " --> pdb=" O TRP A 634 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 659 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 690 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 713 through 717 removed outlier: 3.637A pdb=" N GLU A 724 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 761 through 763 Processing sheet with id= H, first strand: chain 'B' and resid 56 through 58 Processing sheet with id= I, first strand: chain 'B' and resid 91 through 101 removed outlier: 3.973A pdb=" N LEU B 94 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU B 163 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 11.738A pdb=" N LEU B 96 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N TYR B 98 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N LEU B 159 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 11.709A pdb=" N LEU B 100 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 11.109A pdb=" N HIS B 157 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N HIS B 140 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 163 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 12.193A pdb=" N LYS B 138 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 17.317A pdb=" N MET B 165 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 20.533A pdb=" N SER B 136 " --> pdb=" O MET B 165 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B 225 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 145 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 223 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLY B 226 " --> pdb=" O ILE B 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 430 through 434 removed outlier: 3.737A pdb=" N TRP B 442 " --> pdb=" O GLU B 463 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 550 through 553 removed outlier: 3.638A pdb=" N GLY B 556 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 557 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 753 through 757 removed outlier: 6.360A pdb=" N MET B 631 " --> pdb=" O ARG B 754 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N TYR B 756 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 633 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N MET B 732 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TRP B 634 " --> pdb=" O MET B 732 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 734 " --> pdb=" O TRP B 634 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 690 " --> pdb=" O SER B 659 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 713 through 716 Processing sheet with id= N, first strand: chain 'B' and resid 761 through 763 Processing sheet with id= O, first strand: chain 'B' and resid 843 through 845 Processing sheet with id= P, first strand: chain 'B' and resid 893 through 895 Processing sheet with id= Q, first strand: chain 'C' and resid 56 through 58 Processing sheet with id= R, first strand: chain 'C' and resid 91 through 101 removed outlier: 6.360A pdb=" N LEU C 163 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N LEU C 96 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 11.710A pdb=" N TYR C 98 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N LEU C 159 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N LEU C 100 " --> pdb=" O HIS C 157 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N HIS C 157 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS C 140 " --> pdb=" O PRO C 161 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 163 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 11.827A pdb=" N LYS C 138 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 225 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 145 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU C 223 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 230 " --> pdb=" O PRO C 240 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 430 through 434 removed outlier: 3.810A pdb=" N TRP C 442 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 550 through 553 removed outlier: 3.635A pdb=" N GLY C 556 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 557 " --> pdb=" O ILE C 568 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 753 through 757 removed outlier: 6.376A pdb=" N MET C 631 " --> pdb=" O ARG C 754 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR C 756 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU C 633 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET C 732 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TRP C 634 " --> pdb=" O MET C 732 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA C 734 " --> pdb=" O TRP C 634 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 690 " --> pdb=" O SER C 659 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 713 through 717 Processing sheet with id= W, first strand: chain 'C' and resid 761 through 763 Processing sheet with id= X, first strand: chain 'C' and resid 843 through 845 Processing sheet with id= Y, first strand: chain 'C' and resid 893 through 895 Processing sheet with id= Z, first strand: chain 'D' and resid 49 through 51 Processing sheet with id= AA, first strand: chain 'D' and resid 92 through 101 removed outlier: 6.803A pdb=" N LEU D 163 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 11.714A pdb=" N LEU D 96 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 11.961A pdb=" N TYR D 98 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N LEU D 159 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 12.121A pdb=" N LEU D 100 " --> pdb=" O HIS D 157 " (cutoff:3.500A) removed outlier: 11.615A pdb=" N HIS D 157 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N HIS D 140 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU D 163 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N LYS D 138 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 16.539A pdb=" N MET D 165 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 19.506A pdb=" N SER D 136 " --> pdb=" O MET D 165 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS D 137 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 231 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR D 225 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU D 145 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU D 223 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 430 through 434 removed outlier: 3.784A pdb=" N TRP D 442 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 550 through 553 removed outlier: 3.640A pdb=" N GLY D 556 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 557 " --> pdb=" O ILE D 568 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 753 through 757 removed outlier: 6.271A pdb=" N MET D 631 " --> pdb=" O ARG D 754 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N TYR D 756 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU D 633 " --> pdb=" O TYR D 756 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR D 690 " --> pdb=" O SER D 659 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 713 through 717 Processing sheet with id= AF, first strand: chain 'D' and resid 761 through 763 Processing sheet with id= AG, first strand: chain 'D' and resid 843 through 845 Processing sheet with id= AH, first strand: chain 'D' and resid 893 through 895 removed outlier: 3.604A pdb=" N ILE D 902 " --> pdb=" O GLN D 894 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 56 through 58 Processing sheet with id= AJ, first strand: chain 'E' and resid 91 through 101 removed outlier: 6.406A pdb=" N LEU E 163 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N LEU E 96 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N TYR E 98 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N LEU E 159 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 11.309A pdb=" N LEU E 100 " --> pdb=" O HIS E 157 " (cutoff:3.500A) removed outlier: 11.083A pdb=" N HIS E 157 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 159 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N HIS E 140 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU E 163 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 12.246A pdb=" N LYS E 138 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 17.072A pdb=" N MET E 165 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 20.459A pdb=" N SER E 136 " --> pdb=" O MET E 165 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU E 145 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU E 223 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS E 242 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 430 through 434 removed outlier: 3.748A pdb=" N TRP E 442 " --> pdb=" O GLU E 463 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 550 through 553 removed outlier: 3.518A pdb=" N GLY E 556 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 753 through 757 removed outlier: 6.198A pdb=" N MET E 631 " --> pdb=" O ARG E 754 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR E 756 " --> pdb=" O MET E 631 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU E 633 " --> pdb=" O TYR E 756 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N MET E 732 " --> pdb=" O LEU E 632 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N TRP E 634 " --> pdb=" O MET E 732 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA E 734 " --> pdb=" O TRP E 634 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR E 690 " --> pdb=" O SER E 659 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 713 through 717 Processing sheet with id= AO, first strand: chain 'E' and resid 761 through 763 Processing sheet with id= AP, first strand: chain 'E' and resid 843 through 845 removed outlier: 3.536A pdb=" N VAL E 844 " --> pdb=" O ARG E 907 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 893 through 895 removed outlier: 3.592A pdb=" N GLN E 894 " --> pdb=" O ILE E 902 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 56 through 58 Processing sheet with id= AS, first strand: chain 'F' and resid 91 through 101 removed outlier: 6.629A pdb=" N LEU F 163 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 11.050A pdb=" N LEU F 96 " --> pdb=" O PRO F 161 " (cutoff:3.500A) removed outlier: 11.835A pdb=" N TYR F 98 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 11.063A pdb=" N LEU F 159 " --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N LEU F 100 " --> pdb=" O HIS F 157 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N HIS F 157 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N HIS F 140 " --> pdb=" O PRO F 161 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU F 163 " --> pdb=" O LYS F 138 " (cutoff:3.500A) removed outlier: 12.412A pdb=" N LYS F 138 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 16.534A pdb=" N MET F 165 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 20.048A pdb=" N SER F 136 " --> pdb=" O MET F 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 143 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR F 225 " --> pdb=" O PHE F 143 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU F 145 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU F 223 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'F' and resid 430 through 434 removed outlier: 3.646A pdb=" N TRP F 442 " --> pdb=" O GLU F 463 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'F' and resid 550 through 553 removed outlier: 3.592A pdb=" N VAL F 557 " --> pdb=" O ILE F 568 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'F' and resid 753 through 757 removed outlier: 6.440A pdb=" N MET F 631 " --> pdb=" O ARG F 754 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYR F 756 " --> pdb=" O MET F 631 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU F 633 " --> pdb=" O TYR F 756 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 632 " --> pdb=" O MET F 732 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'F' and resid 761 through 763 Processing sheet with id= AX, first strand: chain 'F' and resid 843 through 845 Processing sheet with id= AY, first strand: chain 'F' and resid 893 through 895 1760 hydrogen bonds defined for protein. 5079 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: 17.52 Time building geometry restraints manager: 17.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10608 1.33 - 1.46: 9077 1.46 - 1.58: 21436 1.58 - 1.70: 33 1.70 - 1.83: 230 Bond restraints: 41384 Sorted by residual: bond pdb=" N3B ANP A1001 " pdb=" PG ANP A1001 " ideal model delta sigma weight residual 1.795 1.529 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" N3B ANP C1001 " pdb=" PG ANP C1001 " ideal model delta sigma weight residual 1.795 1.543 0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" N3B ANP B1001 " pdb=" PG ANP B1001 " ideal model delta sigma weight residual 1.795 1.592 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" N3B ANP D1001 " pdb=" PG ANP D1001 " ideal model delta sigma weight residual 1.795 1.595 0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" N3B ANP F1001 " pdb=" PG ANP F1001 " ideal model delta sigma weight residual 1.795 1.597 0.198 2.00e-02 2.50e+03 9.85e+01 ... (remaining 41379 not shown) Histogram of bond angle deviations from ideal: 93.89 - 103.18: 417 103.18 - 112.47: 20914 112.47 - 121.75: 26108 121.75 - 131.04: 8759 131.04 - 140.33: 275 Bond angle restraints: 56473 Sorted by residual: angle pdb=" N3B ANP A1001 " pdb=" PG ANP A1001 " pdb=" O2G ANP A1001 " ideal model delta sigma weight residual 101.05 117.05 -16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" CB HIS C 782 " pdb=" CG HIS C 782 " pdb=" CD2 HIS C 782 " ideal model delta sigma weight residual 131.20 124.75 6.45 1.30e+00 5.92e-01 2.46e+01 angle pdb=" N ARG F 717 " pdb=" CA ARG F 717 " pdb=" C ARG F 717 " ideal model delta sigma weight residual 108.45 114.38 -5.93 1.26e+00 6.30e-01 2.22e+01 angle pdb=" N MET F 732 " pdb=" CA MET F 732 " pdb=" C MET F 732 " ideal model delta sigma weight residual 109.24 116.86 -7.62 1.63e+00 3.76e-01 2.19e+01 angle pdb=" CA LEU E 27 " pdb=" C LEU E 27 " pdb=" N GLU E 28 " ideal model delta sigma weight residual 117.07 122.32 -5.25 1.14e+00 7.69e-01 2.12e+01 ... (remaining 56468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 24161 35.56 - 71.12: 346 71.12 - 106.68: 49 106.68 - 142.24: 3 142.24 - 177.80: 2 Dihedral angle restraints: 24561 sinusoidal: 8364 harmonic: 16197 Sorted by residual: dihedral pdb=" O1A ANP B1001 " pdb=" O3A ANP B1001 " pdb=" PA ANP B1001 " pdb=" PB ANP B1001 " ideal model delta sinusoidal sigma weight residual 83.11 -94.69 177.80 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP A1001 " pdb=" O3A ANP A1001 " pdb=" PA ANP A1001 " pdb=" PB ANP A1001 " ideal model delta sinusoidal sigma weight residual 83.11 -111.20 -165.69 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1A ANP C1001 " pdb=" O3A ANP C1001 " pdb=" PA ANP C1001 " pdb=" PB ANP C1001 " ideal model delta sinusoidal sigma weight residual 83.11 -58.91 142.02 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 24558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 6026 0.129 - 0.257: 229 0.257 - 0.386: 10 0.386 - 0.515: 4 0.515 - 0.644: 2 Chirality restraints: 6271 Sorted by residual: chirality pdb=" P DT G 1 " pdb=" OP1 DT G 1 " pdb=" OP2 DT G 1 " pdb=" O5' DT G 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DT G 2 " pdb=" OP1 DT G 2 " pdb=" OP2 DT G 2 " pdb=" O5' DT G 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" P DT G 3 " pdb=" OP1 DT G 3 " pdb=" OP2 DT G 3 " pdb=" O5' DT G 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 6268 not shown) Planarity restraints: 7315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT G 6 " 0.092 2.00e-02 2.50e+03 6.56e-02 1.07e+02 pdb=" N1 DT G 6 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DT G 6 " -0.023 2.00e-02 2.50e+03 pdb=" O2 DT G 6 " -0.120 2.00e-02 2.50e+03 pdb=" N3 DT G 6 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DT G 6 " 0.035 2.00e-02 2.50e+03 pdb=" O4 DT G 6 " 0.084 2.00e-02 2.50e+03 pdb=" C5 DT G 6 " -0.015 2.00e-02 2.50e+03 pdb=" C7 DT G 6 " -0.099 2.00e-02 2.50e+03 pdb=" C6 DT G 6 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP C1001 " 0.139 2.00e-02 2.50e+03 6.12e-02 1.03e+02 pdb=" C2 ANP C1001 " -0.017 2.00e-02 2.50e+03 pdb=" C4 ANP C1001 " -0.054 2.00e-02 2.50e+03 pdb=" C5 ANP C1001 " -0.044 2.00e-02 2.50e+03 pdb=" C6 ANP C1001 " 0.004 2.00e-02 2.50e+03 pdb=" C8 ANP C1001 " -0.024 2.00e-02 2.50e+03 pdb=" N1 ANP C1001 " 0.054 2.00e-02 2.50e+03 pdb=" N3 ANP C1001 " -0.071 2.00e-02 2.50e+03 pdb=" N6 ANP C1001 " 0.077 2.00e-02 2.50e+03 pdb=" N7 ANP C1001 " -0.040 2.00e-02 2.50e+03 pdb=" N9 ANP C1001 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT G 7 " 0.087 2.00e-02 2.50e+03 5.79e-02 8.39e+01 pdb=" N1 DT G 7 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DT G 7 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DT G 7 " -0.110 2.00e-02 2.50e+03 pdb=" N3 DT G 7 " 0.028 2.00e-02 2.50e+03 pdb=" C4 DT G 7 " 0.028 2.00e-02 2.50e+03 pdb=" O4 DT G 7 " 0.069 2.00e-02 2.50e+03 pdb=" C5 DT G 7 " -0.015 2.00e-02 2.50e+03 pdb=" C7 DT G 7 " -0.083 2.00e-02 2.50e+03 pdb=" C6 DT G 7 " 0.001 2.00e-02 2.50e+03 ... (remaining 7312 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 16 2.27 - 2.93: 16761 2.93 - 3.59: 58957 3.59 - 4.24: 89862 4.24 - 4.90: 151038 Nonbonded interactions: 316634 Sorted by model distance: nonbonded pdb=" O2G ANP B1001 " pdb="MG MG B1002 " model vdw 1.618 2.170 nonbonded pdb=" O3G ANP C1001 " pdb="MG MG C1002 " model vdw 1.879 2.170 nonbonded pdb=" O2B ANP A1001 " pdb="MG MG A1002 " model vdw 1.886 2.170 nonbonded pdb=" O2B ANP C1001 " pdb="MG MG C1002 " model vdw 1.978 2.170 nonbonded pdb=" O2G ANP A1001 " pdb="MG MG A1002 " model vdw 1.979 2.170 ... (remaining 316629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 274 or resid 285 through 293 or (resid 294 and ( \ name N or name CA or name C or name O or name CB )) or resid 295 through 301 or \ (resid 302 and (name N or name CA or name C or name O or name CB )) or resid 303 \ through 315 or (resid 316 through 317 and (name N or name CA or name C or name \ O or name CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or \ name C or name O or name CB )) or resid 337 through 456 or (resid 457 and (name \ N or name CA or name C or name O or name CB )) or resid 458 through 550 or (res \ id 551 and (name N or name CA or name C or name O or name CB )) or resid 552 thr \ ough 600 or (resid 601 and (name N or name CA or name C or name O or name CB )) \ or resid 602 through 680 or (resid 681 and (name N or name CA or name C or name \ O or name CB )) or resid 682 or (resid 683 and (name N or name CA or name C or n \ ame O or name CB )) or resid 684 through 691 or (resid 692 through 693 and (name \ N or name CA or name C or name O or name CB )) or resid 694 through 698 or (res \ id 699 and (name N or name CA or name C or name O or name CB )) or resid 700 thr \ ough 704 or (resid 705 and (name N or name CA or name C or name O or name CB )) \ or resid 706 through 707 or (resid 708 and (name N or name CA or name C or name \ O or name CB )) or resid 709 or (resid 710 and (name N or name CA or name C or n \ ame O or name CB )) or resid 711 through 712 or (resid 713 and (name N or name C \ A or name C or name O or name CB )) or resid 714 through 716 or (resid 717 and ( \ name N or name CA or name C or name O or name CB )) or resid 718 or resid 723 th \ rough 725 or (resid 726 and (name N or name CA or name C or name O or name CB )) \ or resid 727 through 740 or (resid 741 and (name N or name CA or name C or name \ O or name CB )) or resid 742 through 769 or (resid 770 and (name N or name CA o \ r name C or name O or name CB )) or resid 771 through 772 or (resid 773 and (nam \ e N or name CA or name C or name O or name CB )) or resid 774 through 840 or (re \ sid 841 through 842 and (name N or name CA or name C or name O or name CB )) or \ resid 843 through 853 or (resid 854 and (name N or name CA or name C or name O o \ r name CB )) or resid 855 through 858 or (resid 859 and (name N or name CA or na \ me C or name O or name CB )) or resid 860 through 863 or (resid 864 and (name N \ or name CA or name C or name O or name CB )) or resid 865 through 877 or (resid \ 878 and (name N or name CA or name C or name O or name CB )) or resid 879 or (re \ sid 880 and (name N or name CA or name C or name O or name CB )) or resid 881 th \ rough 888 or (resid 889 and (name N or name CA or name C or name O or name CB )) \ or resid 890 or (resid 891 and (name N or name CA or name C or name O or name C \ B )) or resid 892 or (resid 893 through 894 and (name N or name CA or name C or \ name O or name CB )) or resid 895 through 900 or (resid 901 and (name N or name \ CA or name C or name O or name CB )) or resid 902 or (resid 903 through 904 and \ (name N or name CA or name C or name O or name CB )) or resid 905 through 906 or \ (resid 907 through 908 and (name N or name CA or name C or name O or name CB )) \ or resid 909 through 914 or (resid 915 and (name N or name CA or name C or name \ O or name CB )) or resid 916 through 949)) selection = (chain 'B' and (resid 9 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or name \ CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or name C o \ r name O or name CB )) or resid 337 through 358 or (resid 359 and (name N or nam \ e CA or name C or name O or name CB )) or resid 360 through 366 or (resid 367 th \ rough 368 and (name N or name CA or name C or name O or name CB )) or resid 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 413 or (resid 414 and (name N or name CA or name C or na \ me O or name CB )) or resid 415 through 456 or (resid 457 and (name N or name CA \ or name C or name O or name CB )) or resid 458 through 550 or (resid 551 and (n \ ame N or name CA or name C or name O or name CB )) or resid 552 through 600 or ( \ resid 601 and (name N or name CA or name C or name O or name CB )) or resid 602 \ through 666 or (resid 667 and (name N or name CA or name C or name O or name CB \ )) or resid 668 through 670 or (resid 671 through 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 680 or (resid 681 and (name \ N or name CA or name C or name O or name CB )) or resid 682 or (resid 683 and (n \ ame N or name CA or name C or name O or name CB )) or resid 684 through 691 or ( \ resid 692 through 693 and (name N or name CA or name C or name O or name CB )) o \ r resid 694 through 698 or (resid 699 and (name N or name CA or name C or name O \ or name CB )) or resid 700 through 704 or (resid 705 and (name N or name CA or \ name C or name O or name CB )) or resid 706 through 707 or (resid 708 and (name \ N or name CA or name C or name O or name CB )) or resid 709 or (resid 710 and (n \ ame N or name CA or name C or name O or name CB )) or resid 711 through 712 or ( \ resid 713 and (name N or name CA or name C or name O or name CB )) or resid 714 \ through 716 or (resid 717 and (name N or name CA or name C or name O or name CB \ )) or resid 718 or resid 723 through 725 or (resid 726 and (name N or name CA or \ name C or name O or name CB )) or resid 727 or (resid 728 and (name N or name C \ A or name C or name O or name CB )) or resid 729 through 740 or (resid 741 and ( \ name N or name CA or name C or name O or name CB )) or resid 742 through 769 or \ (resid 770 and (name N or name CA or name C or name O or name CB )) or resid 771 \ through 772 or (resid 773 and (name N or name CA or name C or name O or name CB \ )) or resid 774 through 780 or (resid 781 and (name N or name CA or name C or n \ ame O or name CB )) or resid 782 through 813 or (resid 814 and (name N or name C \ A or name C or name O or name CB )) or resid 815 through 834 or (resid 835 and ( \ name N or name CA or name C or name O or name CB )) or resid 836 through 840 or \ (resid 841 through 842 and (name N or name CA or name C or name O or name CB )) \ or resid 843 through 851 or (resid 852 and (name N or name CA or name C or name \ O or name CB )) or resid 853 or (resid 854 and (name N or name CA or name C or n \ ame O or name CB )) or resid 855 through 857 or (resid 858 through 859 and (name \ N or name CA or name C or name O or name CB )) or resid 860 through 863 or (res \ id 864 and (name N or name CA or name C or name O or name CB )) or resid 865 or \ (resid 866 and (name N or name CA or name C or name O or name CB )) or resid 867 \ through 877 or (resid 878 and (name N or name CA or name C or name O or name CB \ )) or resid 879 or (resid 880 and (name N or name CA or name C or name O or nam \ e CB )) or resid 881 through 883 or (resid 884 and (name N or name CA or name C \ or name O or name CB )) or resid 885 through 888 or (resid 889 and (name N or na \ me CA or name C or name O or name CB )) or resid 890 through 892 or (resid 893 t \ hrough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 \ through 900 or (resid 901 and (name N or name CA or name C or name O or name CB \ )) or resid 902 or (resid 903 through 904 and (name N or name CA or name C or n \ ame O or name CB )) or resid 905 through 907 or (resid 908 and (name N or name C \ A or name C or name O or name CB )) or resid 909 through 914 or (resid 915 and ( \ name N or name CA or name C or name O or name CB )) or resid 916 through 947 or \ (resid 948 through 949 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'C' and (resid 9 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or name \ CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or name C o \ r name O or name CB )) or resid 337 through 358 or (resid 359 and (name N or nam \ e CA or name C or name O or name CB )) or resid 360 through 366 or (resid 367 th \ rough 368 and (name N or name CA or name C or name O or name CB )) or resid 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 393 or (resid 394 and (name N or name CA or name C or na \ me O or name CB )) or resid 395 through 413 or (resid 414 and (name N or name CA \ or name C or name O or name CB )) or resid 415 through 456 or (resid 457 and (n \ ame N or name CA or name C or name O or name CB )) or resid 458 through 550 or ( \ resid 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 575 or (resid 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 600 or (resid 601 and (name N or name CA or name C or na \ me O or name CB )) or resid 602 through 666 or (resid 667 and (name N or name CA \ or name C or name O or name CB )) or resid 668 through 670 or (resid 671 throug \ h 674 and (name N or name CA or name C or name O or name CB )) or resid 675 thro \ ugh 680 or (resid 681 and (name N or name CA or name C or name O or name CB )) o \ r resid 682 or (resid 683 and (name N or name CA or name C or name O or name CB \ )) or resid 684 through 691 or (resid 692 through 693 and (name N or name CA or \ name C or name O or name CB )) or resid 694 through 698 or (resid 699 and (name \ N or name CA or name C or name O or name CB )) or resid 700 through 707 or (resi \ d 708 and (name N or name CA or name C or name O or name CB )) or resid 709 or ( \ resid 710 and (name N or name CA or name C or name O or name CB )) or resid 711 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 716 or (resid 717 and (name N or name CA or name C or na \ me O or name CB )) or resid 718 or resid 723 through 725 or (resid 726 and (name \ N or name CA or name C or name O or name CB )) or resid 727 or (resid 728 and ( \ name N or name CA or name C or name O or name CB )) or resid 729 through 740 or \ (resid 741 and (name N or name CA or name C or name O or name CB )) or resid 742 \ through 769 or (resid 770 and (name N or name CA or name C or name O or name CB \ )) or resid 771 through 772 or (resid 773 and (name N or name CA or name C or n \ ame O or name CB )) or resid 774 through 780 or (resid 781 and (name N or name C \ A or name C or name O or name CB )) or resid 782 through 813 or (resid 814 and ( \ name N or name CA or name C or name O or name CB )) or resid 815 through 834 or \ (resid 835 and (name N or name CA or name C or name O or name CB )) or resid 836 \ through 840 or (resid 841 through 842 and (name N or name CA or name C or name \ O or name CB )) or resid 843 through 851 or (resid 852 and (name N or name CA or \ name C or name O or name CB )) or resid 853 or (resid 854 and (name N or name C \ A or name C or name O or name CB )) or resid 855 through 858 or (resid 859 and ( \ name N or name CA or name C or name O or name CB )) or resid 860 through 863 or \ (resid 864 and (name N or name CA or name C or name O or name CB )) or resid 865 \ or (resid 866 and (name N or name CA or name C or name O or name CB )) or resid \ 867 through 877 or (resid 878 and (name N or name CA or name C or name O or nam \ e CB )) or resid 879 or (resid 880 and (name N or name CA or name C or name O or \ name CB )) or resid 881 through 890 or (resid 891 and (name N or name CA or nam \ e C or name O or name CB )) or resid 892 through 893 or (resid 894 and (name N o \ r name CA or name C or name O or name CB )) or resid 895 through 902 or (resid 9 \ 03 through 904 and (name N or name CA or name C or name O or name CB )) or resid \ 905 through 906 or (resid 907 through 908 and (name N or name CA or name C or n \ ame O or name CB )) or resid 909 through 918 or resid 936 through 947 or (resid \ 948 through 949 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 9 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or name \ CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or name C o \ r name O or name CB )) or resid 337 through 358 or (resid 359 and (name N or nam \ e CA or name C or name O or name CB )) or resid 360 through 366 or (resid 367 th \ rough 368 and (name N or name CA or name C or name O or name CB )) or resid 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 413 or (resid 414 and (name N or name CA or name C or na \ me O or name CB )) or resid 415 through 456 or (resid 457 and (name N or name CA \ or name C or name O or name CB )) or resid 458 through 550 or (resid 551 and (n \ ame N or name CA or name C or name O or name CB )) or resid 552 through 575 or ( \ resid 576 and (name N or name CA or name C or name O or name CB )) or resid 577 \ through 600 or (resid 601 and (name N or name CA or name C or name O or name CB \ )) or resid 602 through 666 or (resid 667 and (name N or name CA or name C or na \ me O or name CB )) or resid 668 through 670 or (resid 671 through 674 and (name \ N or name CA or name C or name O or name CB )) or resid 675 through 680 or (resi \ d 681 and (name N or name CA or name C or name O or name CB )) or resid 682 thro \ ugh 692 or (resid 693 and (name N or name CA or name C or name O or name CB )) o \ r resid 694 through 698 or (resid 699 and (name N or name CA or name C or name O \ or name CB )) or resid 700 through 704 or (resid 705 and (name N or name CA or \ name C or name O or name CB )) or resid 706 through 709 or (resid 710 and (name \ N or name CA or name C or name O or name CB )) or resid 711 through 712 or (resi \ d 713 and (name N or name CA or name C or name O or name CB )) or resid 714 thro \ ugh 716 or (resid 717 and (name N or name CA or name C or name O or name CB )) o \ r resid 718 or resid 723 through 725 or (resid 726 and (name N or name CA or nam \ e C or name O or name CB )) or resid 727 or (resid 728 and (name N or name CA or \ name C or name O or name CB )) or resid 729 through 740 or (resid 741 and (name \ N or name CA or name C or name O or name CB )) or resid 742 through 769 or (res \ id 770 and (name N or name CA or name C or name O or name CB )) or resid 771 thr \ ough 772 or (resid 773 and (name N or name CA or name C or name O or name CB )) \ or resid 774 through 780 or (resid 781 and (name N or name CA or name C or name \ O or name CB )) or resid 782 through 813 or (resid 814 and (name N or name CA or \ name C or name O or name CB )) or resid 815 through 834 or (resid 835 and (name \ N or name CA or name C or name O or name CB )) or resid 836 or (resid 837 and ( \ name N or name CA or name C or name O or name CB )) or resid 838 through 840 or \ (resid 841 through 842 and (name N or name CA or name C or name O or name CB )) \ or resid 843 through 851 or (resid 852 and (name N or name CA or name C or name \ O or name CB )) or resid 853 or (resid 854 and (name N or name CA or name C or n \ ame O or name CB )) or resid 855 through 857 or (resid 858 through 859 and (name \ N or name CA or name C or name O or name CB )) or resid 860 through 863 or (res \ id 864 and (name N or name CA or name C or name O or name CB )) or resid 865 or \ (resid 866 and (name N or name CA or name C or name O or name CB )) or resid 867 \ through 877 or (resid 878 and (name N or name CA or name C or name O or name CB \ )) or resid 879 or (resid 880 and (name N or name CA or name C or name O or nam \ e CB )) or resid 881 through 883 or (resid 884 and (name N or name CA or name C \ or name O or name CB )) or resid 885 through 888 or (resid 889 and (name N or na \ me CA or name C or name O or name CB )) or resid 890 or (resid 891 and (name N o \ r name CA or name C or name O or name CB )) or resid 892 or (resid 893 through 8 \ 94 and (name N or name CA or name C or name O or name CB )) or resid 895 through \ 900 or (resid 901 and (name N or name CA or name C or name O or name CB )) or r \ esid 902 or (resid 903 through 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 906 or (resid 907 through 908 and (name N or na \ me CA or name C or name O or name CB )) or resid 909 through 914 or (resid 915 a \ nd (name N or name CA or name C or name O or name CB )) or resid 916 through 918 \ or resid 936 through 947 or (resid 948 through 949 and (name N or name CA or na \ me C or name O or name CB )))) selection = (chain 'E' and (resid 9 through 358 or (resid 359 and (name N or name CA or name \ C or name O or name CB )) or resid 360 through 366 or (resid 367 through 368 an \ d (name N or name CA or name C or name O or name CB )) or resid 369 or (resid 37 \ 0 through 371 and (name N or name CA or name C or name O or name CB )) or resid \ 372 through 393 or (resid 394 and (name N or name CA or name C or name O or name \ CB )) or resid 395 through 413 or (resid 414 and (name N or name CA or name C o \ r name O or name CB )) or resid 415 through 575 or (resid 576 and (name N or nam \ e CA or name C or name O or name CB )) or resid 577 through 600 or (resid 601 an \ d (name N or name CA or name C or name O or name CB )) or resid 602 through 666 \ or (resid 667 and (name N or name CA or name C or name O or name CB )) or resid \ 668 through 670 or (resid 671 through 674 and (name N or name CA or name C or na \ me O or name CB )) or resid 675 through 680 or (resid 681 and (name N or name CA \ or name C or name O or name CB )) or resid 682 or (resid 683 and (name N or nam \ e CA or name C or name O or name CB )) or resid 684 through 691 or (resid 692 th \ rough 693 and (name N or name CA or name C or name O or name CB )) or resid 694 \ through 704 or (resid 705 and (name N or name CA or name C or name O or name CB \ )) or resid 706 through 707 or (resid 708 and (name N or name CA or name C or na \ me O or name CB )) or resid 709 through 712 or (resid 713 and (name N or name CA \ or name C or name O or name CB )) or resid 714 through 716 or (resid 717 and (n \ ame N or name CA or name C or name O or name CB )) or resid 718 or resid 723 thr \ ough 725 or (resid 726 and (name N or name CA or name C or name O or name CB )) \ or resid 727 or (resid 728 and (name N or name CA or name C or name O or name CB \ )) or resid 729 through 769 or (resid 770 and (name N or name CA or name C or n \ ame O or name CB )) or resid 771 through 772 or (resid 773 and (name N or name C \ A or name C or name O or name CB )) or resid 774 through 780 or (resid 781 and ( \ name N or name CA or name C or name O or name CB )) or resid 782 through 813 or \ (resid 814 and (name N or name CA or name C or name O or name CB )) or resid 815 \ through 834 or (resid 835 and (name N or name CA or name C or name O or name CB \ )) or resid 836 or (resid 837 and (name N or name CA or name C or name O or nam \ e CB )) or resid 838 through 851 or (resid 852 and (name N or name CA or name C \ or name O or name CB )) or resid 853 through 857 or (resid 858 through 859 and ( \ name N or name CA or name C or name O or name CB )) or resid 860 through 865 or \ (resid 866 and (name N or name CA or name C or name O or name CB )) or resid 867 \ through 883 or (resid 884 and (name N or name CA or name C or name O or name CB \ )) or resid 885 through 888 or (resid 889 and (name N or name CA or name C or n \ ame O or name CB )) or resid 890 or (resid 891 and (name N or name CA or name C \ or name O or name CB )) or resid 892 or (resid 893 through 894 and (name N or na \ me CA or name C or name O or name CB )) or resid 895 through 900 or (resid 901 a \ nd (name N or name CA or name C or name O or name CB )) or resid 902 through 903 \ or (resid 904 and (name N or name CA or name C or name O or name CB )) or resid \ 905 through 906 or (resid 907 through 908 and (name N or name CA or name C or n \ ame O or name CB )) or resid 909 through 914 or (resid 915 and (name N or name C \ A or name C or name O or name CB )) or resid 916 through 918 or resid 936 throug \ h 947 or (resid 948 through 949 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'F' and (resid 9 through 289 or (resid 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 through 301 or (resid 30 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 303 through \ 315 or (resid 316 through 317 and (name N or name CA or name C or name O or name \ CB )) or resid 318 through 335 or (resid 336 and (name N or name CA or name C o \ r name O or name CB )) or resid 337 through 358 or (resid 359 and (name N or nam \ e CA or name C or name O or name CB )) or resid 360 through 366 or (resid 367 th \ rough 368 and (name N or name CA or name C or name O or name CB )) or resid 369 \ or (resid 370 through 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 393 or (resid 394 and (name N or name CA or name C or na \ me O or name CB )) or resid 395 through 413 or (resid 414 and (name N or name CA \ or name C or name O or name CB )) or resid 415 through 456 or (resid 457 and (n \ ame N or name CA or name C or name O or name CB )) or resid 458 through 550 or ( \ resid 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 575 or (resid 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 666 or (resid 667 and (name N or name CA or name C or na \ me O or name CB )) or resid 668 through 670 or (resid 671 through 674 and (name \ N or name CA or name C or name O or name CB )) or resid 675 through 682 or (resi \ d 683 and (name N or name CA or name C or name O or name CB )) or resid 684 thro \ ugh 691 or (resid 692 through 693 and (name N or name CA or name C or name O or \ name CB )) or resid 694 through 698 or (resid 699 and (name N or name CA or name \ C or name O or name CB )) or resid 700 through 704 or (resid 705 and (name N or \ name CA or name C or name O or name CB )) or resid 706 through 707 or (resid 70 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 709 or (resi \ d 710 and (name N or name CA or name C or name O or name CB )) or resid 711 thro \ ugh 740 or (resid 741 and (name N or name CA or name C or name O or name CB )) o \ r resid 742 through 780 or (resid 781 and (name N or name CA or name C or name O \ or name CB )) or resid 782 through 813 or (resid 814 and (name N or name CA or \ name C or name O or name CB )) or resid 815 through 834 or (resid 835 and (name \ N or name CA or name C or name O or name CB )) or resid 836 or (resid 837 and (n \ ame N or name CA or name C or name O or name CB )) or resid 838 through 840 or ( \ resid 841 through 842 and (name N or name CA or name C or name O or name CB )) o \ r resid 843 through 851 or (resid 852 and (name N or name CA or name C or name O \ or name CB )) or resid 853 or (resid 854 and (name N or name CA or name C or na \ me O or name CB )) or resid 855 through 857 or (resid 858 through 859 and (name \ N or name CA or name C or name O or name CB )) or resid 860 through 863 or (resi \ d 864 and (name N or name CA or name C or name O or name CB )) or resid 865 or ( \ resid 866 and (name N or name CA or name C or name O or name CB )) or resid 867 \ through 877 or (resid 878 and (name N or name CA or name C or name O or name CB \ )) or resid 879 or (resid 880 and (name N or name CA or name C or name O or name \ CB )) or resid 881 through 883 or (resid 884 and (name N or name CA or name C o \ r name O or name CB )) or resid 885 through 888 or (resid 889 and (name N or nam \ e CA or name C or name O or name CB )) or resid 890 or (resid 891 and (name N or \ name CA or name C or name O or name CB )) or resid 892 or (resid 893 through 89 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 895 through \ 900 or (resid 901 and (name N or name CA or name C or name O or name CB )) or re \ sid 902 or (resid 903 through 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 906 or (resid 907 through 908 and (name N or nam \ e CA or name C or name O or name CB )) or resid 909 through 914 or (resid 915 an \ d (name N or name CA or name C or name O or name CB )) or resid 916 through 947 \ or (resid 948 through 949 and (name N or name CA or name C or name O or name CB \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.070 Check model and map are aligned: 0.580 Set scattering table: 0.400 Process input model: 109.060 Find NCS groups from input model: 3.980 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 0.266 41384 Z= 0.436 Angle : 0.943 15.999 56473 Z= 0.595 Chirality : 0.058 0.644 6271 Planarity : 0.007 0.118 7315 Dihedral : 13.720 177.797 14053 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.64 % Allowed : 0.64 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.11), residues: 5450 helix: 1.67 (0.11), residues: 2498 sheet: 0.79 (0.22), residues: 552 loop : 0.12 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.006 TRP F 634 HIS 0.014 0.001 HIS F 577 PHE 0.086 0.003 PHE E 680 TYR 0.110 0.005 TYR A 669 ARG 0.013 0.001 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10900 Ramachandran restraints generated. 5450 Oldfield, 0 Emsley, 5450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 462 time to evaluate : 4.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 HIS cc_start: 0.8849 (m90) cc_final: 0.8414 (m90) REVERT: A 426 MET cc_start: 0.7725 (mmm) cc_final: 0.7513 (mmm) REVERT: B 862 TYR cc_start: 0.8606 (t80) cc_final: 0.8318 (t80) REVERT: C 718 GLU cc_start: 0.6184 (tp30) cc_final: 0.5524 (tp30) REVERT: C 722 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8669 (mtmm) REVERT: D 335 TYR cc_start: 0.8497 (m-10) cc_final: 0.8225 (m-10) REVERT: E 395 GLU cc_start: 0.8298 (tp30) cc_final: 0.8034 (tp30) REVERT: E 948 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7850 (p0) REVERT: F 288 HIS cc_start: 0.8308 (m90) cc_final: 0.7584 (m-70) REVERT: F 551 LEU cc_start: 0.9011 (tp) cc_final: 0.8770 (tp) outliers start: 22 outliers final: 2 residues processed: 480 average time/residue: 0.6264 time to fit residues: 470.2743 Evaluate side-chains 280 residues out of total 4948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 277 time to evaluate : 4.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 691 PHE Chi-restraints excluded: chain E residue 948 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 547 random chunks: chunk 461 optimal weight: 6.9990 chunk 414 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 428 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 496 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN B 720 ASN B 769 ASN C 368 HIS C 727 GLN C 765 ASN C 769 ASN D 308 ASN D 765 ASN D 782 HIS E 304 HIS E 389 GLN E 437 ASN E 542 GLN F 491 HIS F 662 ASN F 836 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1556 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: