Starting phenix.real_space_refine on Fri Dec 8 08:40:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jgz_9824/12_2023/6jgz_9824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jgz_9824/12_2023/6jgz_9824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jgz_9824/12_2023/6jgz_9824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jgz_9824/12_2023/6jgz_9824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jgz_9824/12_2023/6jgz_9824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jgz_9824/12_2023/6jgz_9824.pdb" } resolution = 4.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 648 5.16 5 C 69896 2.51 5 N 18800 2.21 5 O 20476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2323": "NH1" <-> "NH2" Residue "B ARG 2519": "NH1" <-> "NH2" Residue "B ARG 3616": "NH1" <-> "NH2" Residue "B PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4148": "NH1" <-> "NH2" Residue "B ARG 4158": "NH1" <-> "NH2" Residue "B ARG 4498": "NH1" <-> "NH2" Residue "B ARG 4504": "NH1" <-> "NH2" Residue "B TYR 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4791": "NH1" <-> "NH2" Residue "B ARG 4875": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2323": "NH1" <-> "NH2" Residue "D ARG 2519": "NH1" <-> "NH2" Residue "D ARG 3616": "NH1" <-> "NH2" Residue "D PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4148": "NH1" <-> "NH2" Residue "D ARG 4158": "NH1" <-> "NH2" Residue "D ARG 4498": "NH1" <-> "NH2" Residue "D ARG 4504": "NH1" <-> "NH2" Residue "D TYR 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4791": "NH1" <-> "NH2" Residue "D ARG 4875": "NH1" <-> "NH2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "E PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F ARG 257": "NH1" <-> "NH2" Residue "F TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 2323": "NH1" <-> "NH2" Residue "F ARG 2519": "NH1" <-> "NH2" Residue "F ARG 3616": "NH1" <-> "NH2" Residue "F PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 4148": "NH1" <-> "NH2" Residue "F ARG 4158": "NH1" <-> "NH2" Residue "F ARG 4498": "NH1" <-> "NH2" Residue "F ARG 4504": "NH1" <-> "NH2" Residue "F TYR 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 4791": "NH1" <-> "NH2" Residue "F ARG 4875": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 190": "NH1" <-> "NH2" Residue "H ARG 257": "NH1" <-> "NH2" Residue "H TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 1590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 2039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 2323": "NH1" <-> "NH2" Residue "H ARG 2519": "NH1" <-> "NH2" Residue "H ARG 3616": "NH1" <-> "NH2" Residue "H PHE 3637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 4148": "NH1" <-> "NH2" Residue "H ARG 4158": "NH1" <-> "NH2" Residue "H ARG 4498": "NH1" <-> "NH2" Residue "H ARG 4504": "NH1" <-> "NH2" Residue "H TYR 4568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 4791": "NH1" <-> "NH2" Residue "H ARG 4875": "NH1" <-> "NH2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 109824 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 26636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3485, 26636 Classifications: {'peptide': 3485} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 333} Link IDs: {'CIS': 19, 'PTRANS': 118, 'TRANS': 3347} Chain breaks: 59 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1396 Unresolved non-hydrogen angles: 1778 Unresolved non-hydrogen dihedrals: 1166 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 21, 'GLU:plan': 33, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 785 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 26636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3485, 26636 Classifications: {'peptide': 3485} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 333} Link IDs: {'CIS': 19, 'PTRANS': 118, 'TRANS': 3347} Chain breaks: 59 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1396 Unresolved non-hydrogen angles: 1778 Unresolved non-hydrogen dihedrals: 1166 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 21, 'GLU:plan': 33, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 785 Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 26636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3485, 26636 Classifications: {'peptide': 3485} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 333} Link IDs: {'CIS': 19, 'PTRANS': 118, 'TRANS': 3347} Chain breaks: 59 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1396 Unresolved non-hydrogen angles: 1778 Unresolved non-hydrogen dihedrals: 1166 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 21, 'GLU:plan': 33, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 785 Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 26636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3485, 26636 Classifications: {'peptide': 3485} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 333} Link IDs: {'CIS': 19, 'PTRANS': 118, 'TRANS': 3347} Chain breaks: 59 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1396 Unresolved non-hydrogen angles: 1778 Unresolved non-hydrogen dihedrals: 1165 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 21, 'GLU:plan': 33, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 785 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 27399 SG CYS B4958 200.597 198.670 92.082 1.00167.26 S ATOM 54854 SG CYS D4958 198.652 173.071 92.072 1.00167.26 S ATOM 82309 SG CYS F4958 173.068 175.007 92.082 1.00167.26 S ATOM A07J8 SG CYS H4958 175.000 200.617 92.085 1.00167.26 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N HIS A 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS A 87 " occ=0.99 residue: pdb=" N HIS C 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS C 87 " occ=0.99 residue: pdb=" N HIS E 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS E 87 " occ=0.99 residue: pdb=" N HIS G 87 " occ=0.99 ... (8 atoms not shown) pdb=" NE2 HIS G 87 " occ=0.99 Time building chain proxies: 41.61, per 1000 atoms: 0.38 Number of scatterers: 109824 At special positions: 0 Unit cell: (374.977, 374.977, 207.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 648 16.00 O 20476 8.00 N 18800 7.00 C 69896 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: 31.70 Conformation dependent library (CDL) restraints added in 15.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4914 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4958 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4914 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4958 " pdb=" ZN F6000 " pdb="ZN ZN F6000 " - pdb=" NE2 HIS F4914 " pdb="ZN ZN F6000 " - pdb=" SG CYS F4958 " pdb=" ZN H6000 " pdb="ZN ZN H6000 " - pdb=" NE2 HIS H4914 " pdb="ZN ZN H6000 " - pdb=" SG CYS H4958 " 27760 Ramachandran restraints generated. 13880 Oldfield, 0 Emsley, 13880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26928 Finding SS restraints... Secondary structure from input PDB file: 528 helices and 104 sheets defined 52.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.36 Creating SS restraints... Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.985A pdb=" N GLY A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.923A pdb=" N ALA B 105 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 106 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 409 through 439 removed outlier: 4.298A pdb=" N VAL B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 428 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.638A pdb=" N PHE B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 506 removed outlier: 4.105A pdb=" N LEU B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 removed outlier: 3.524A pdb=" N LEU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 removed outlier: 4.028A pdb=" N CYS B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 563 removed outlier: 4.108A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.697A pdb=" N ILE B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.654A pdb=" N ILE B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.578A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 619 removed outlier: 3.614A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 821 through 826 removed outlier: 3.503A pdb=" N VAL B 826 " --> pdb=" O TYR B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 900 Processing helix chain 'B' and resid 929 through 946 removed outlier: 3.996A pdb=" N MET B 935 " --> pdb=" O TYR B 931 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 940 " --> pdb=" O SER B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1011 removed outlier: 3.622A pdb=" N GLU B 993 " --> pdb=" O THR B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1059 removed outlier: 4.227A pdb=" N ASN B1046 " --> pdb=" O THR B1042 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B1050 " --> pdb=" O ASN B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1095 removed outlier: 3.626A pdb=" N ALA B1095 " --> pdb=" O LYS B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1224 Processing helix chain 'B' and resid 1570 through 1576 removed outlier: 3.526A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) Processing helix chain 'B' and resid 1643 through 1646 Processing helix chain 'B' and resid 1647 through 1665 Processing helix chain 'B' and resid 1669 through 1681 removed outlier: 3.606A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B1681 " --> pdb=" O CYS B1677 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 removed outlier: 3.707A pdb=" N GLU B1690 " --> pdb=" O LEU B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1695 through 1711 removed outlier: 3.750A pdb=" N ILE B1707 " --> pdb=" O TYR B1703 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1722 Processing helix chain 'B' and resid 1730 through 1735 Processing helix chain 'B' and resid 1783 through 1803 removed outlier: 3.972A pdb=" N ALA B1789 " --> pdb=" O ASP B1785 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1831 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1900 through 1947 removed outlier: 3.562A pdb=" N LYS B1904 " --> pdb=" O PRO B1900 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B1909 " --> pdb=" O LEU B1905 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B1910 " --> pdb=" O GLN B1906 " (cutoff:3.500A) Processing helix chain 'B' and resid 1999 through 2012 Processing helix chain 'B' and resid 2024 through 2039 removed outlier: 4.128A pdb=" N TYR B2039 " --> pdb=" O GLU B2035 " (cutoff:3.500A) Processing helix chain 'B' and resid 2059 through 2074 removed outlier: 3.633A pdb=" N GLU B2073 " --> pdb=" O ARG B2069 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER B2074 " --> pdb=" O TRP B2070 " (cutoff:3.500A) Processing helix chain 'B' and resid 2078 through 2093 removed outlier: 3.521A pdb=" N VAL B2082 " --> pdb=" O ASP B2078 " (cutoff:3.500A) Processing helix chain 'B' and resid 2096 through 2106 removed outlier: 3.814A pdb=" N ALA B2102 " --> pdb=" O GLY B2098 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B2103 " --> pdb=" O LEU B2099 " (cutoff:3.500A) Proline residue: B2104 - end of helix Processing helix chain 'B' and resid 2113 through 2132 removed outlier: 3.669A pdb=" N THR B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) Processing helix chain 'B' and resid 2139 through 2151 Processing helix chain 'B' and resid 2160 through 2167 removed outlier: 3.907A pdb=" N ARG B2164 " --> pdb=" O PRO B2160 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2180 Processing helix chain 'B' and resid 2192 through 2206 removed outlier: 3.622A pdb=" N PHE B2200 " --> pdb=" O ASN B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2208 through 2216 removed outlier: 3.555A pdb=" N MET B2215 " --> pdb=" O ASN B2211 " (cutoff:3.500A) Processing helix chain 'B' and resid 2218 through 2223 Processing helix chain 'B' and resid 2239 through 2247 removed outlier: 3.537A pdb=" N SER B2247 " --> pdb=" O VAL B2243 " (cutoff:3.500A) Processing helix chain 'B' and resid 2251 through 2258 Processing helix chain 'B' and resid 2259 through 2269 removed outlier: 4.067A pdb=" N LEU B2263 " --> pdb=" O ARG B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2295 through 2308 removed outlier: 3.661A pdb=" N TYR B2299 " --> pdb=" O GLU B2295 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) Processing helix chain 'B' and resid 2315 through 2328 Processing helix chain 'B' and resid 2344 through 2349 removed outlier: 3.602A pdb=" N GLU B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) Processing helix chain 'B' and resid 2387 through 2401 Processing helix chain 'B' and resid 2417 through 2426 removed outlier: 4.317A pdb=" N ILE B2423 " --> pdb=" O ARG B2419 " (cutoff:3.500A) Processing helix chain 'B' and resid 2432 through 2442 removed outlier: 4.043A pdb=" N PHE B2441 " --> pdb=" O ILE B2437 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN B2442 " --> pdb=" O SER B2438 " (cutoff:3.500A) Processing helix chain 'B' and resid 2462 through 2477 removed outlier: 3.845A pdb=" N LYS B2466 " --> pdb=" O CYS B2462 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B2467 " --> pdb=" O PRO B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2482 through 2487 Processing helix chain 'B' and resid 2493 through 2499 Processing helix chain 'B' and resid 2500 through 2502 No H-bonds generated for 'chain 'B' and resid 2500 through 2502' Processing helix chain 'B' and resid 2512 through 2524 removed outlier: 3.930A pdb=" N ASN B2518 " --> pdb=" O ALA B2514 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B2521 " --> pdb=" O LEU B2517 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N CYS B2522 " --> pdb=" O ASN B2518 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B2523 " --> pdb=" O ARG B2519 " (cutoff:3.500A) Processing helix chain 'B' and resid 2525 through 2529 removed outlier: 3.772A pdb=" N LEU B2529 " --> pdb=" O LEU B2526 " (cutoff:3.500A) Processing helix chain 'B' and resid 2535 through 2553 removed outlier: 4.023A pdb=" N THR B2539 " --> pdb=" O LEU B2535 " (cutoff:3.500A) Processing helix chain 'B' and resid 2559 through 2575 removed outlier: 3.637A pdb=" N LYS B2564 " --> pdb=" O CYS B2560 " (cutoff:3.500A) Processing helix chain 'B' and resid 2583 through 2601 removed outlier: 3.700A pdb=" N ARG B2592 " --> pdb=" O HIS B2588 " (cutoff:3.500A) Proline residue: B2598 - end of helix Processing helix chain 'B' and resid 2606 through 2622 removed outlier: 3.584A pdb=" N ARG B2617 " --> pdb=" O ASN B2613 " (cutoff:3.500A) Processing helix chain 'B' and resid 2635 through 2650 Processing helix chain 'B' and resid 2651 through 2653 No H-bonds generated for 'chain 'B' and resid 2651 through 2653' Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2668 - end of helix Processing helix chain 'B' and resid 2715 through 2740 removed outlier: 3.587A pdb=" N GLU B2719 " --> pdb=" O PRO B2715 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE B2721 " --> pdb=" O LYS B2717 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B2724 " --> pdb=" O TYR B2720 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU B2727 " --> pdb=" O ASN B2723 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2786 removed outlier: 4.644A pdb=" N TYR B2772 " --> pdb=" O GLU B2768 " (cutoff:3.500A) Proline residue: B2775 - end of helix Processing helix chain 'B' and resid 2835 through 2865 removed outlier: 3.844A pdb=" N GLU B2860 " --> pdb=" O LYS B2856 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B2862 " --> pdb=" O LYS B2858 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER B2863 " --> pdb=" O LEU B2859 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B2864 " --> pdb=" O GLU B2860 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B2865 " --> pdb=" O LEU B2861 " (cutoff:3.500A) Processing helix chain 'B' and resid 2880 through 2900 removed outlier: 4.115A pdb=" N ASP B2886 " --> pdb=" O GLU B2882 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B2889 " --> pdb=" O LYS B2885 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B2894 " --> pdb=" O ALA B2890 " (cutoff:3.500A) Processing helix chain 'B' and resid 2983 through 3003 Proline residue: B2990 - end of helix Processing helix chain 'B' and resid 3010 through 3027 Processing helix chain 'B' and resid 3035 through 3049 Processing helix chain 'B' and resid 3051 through 3055 removed outlier: 3.839A pdb=" N VAL B3054 " --> pdb=" O LEU B3051 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B3055 " --> pdb=" O GLU B3052 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3051 through 3055' Processing helix chain 'B' and resid 3062 through 3079 Processing helix chain 'B' and resid 3101 through 3117 removed outlier: 3.784A pdb=" N MET B3105 " --> pdb=" O ALA B3101 " (cutoff:3.500A) Processing helix chain 'B' and resid 3125 through 3144 Processing helix chain 'B' and resid 3150 through 3164 Processing helix chain 'B' and resid 3171 through 3181 Processing helix chain 'B' and resid 3614 through 3629 Processing helix chain 'B' and resid 3637 through 3646 Processing helix chain 'B' and resid 3663 through 3677 Processing helix chain 'B' and resid 3686 through 3698 Processing helix chain 'B' and resid 3715 through 3734 Processing helix chain 'B' and resid 3736 through 3748 removed outlier: 3.657A pdb=" N MET B3740 " --> pdb=" O GLY B3736 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B3741 " --> pdb=" O ALA B3737 " (cutoff:3.500A) Processing helix chain 'B' and resid 3753 through 3767 removed outlier: 3.679A pdb=" N ALA B3765 " --> pdb=" O LYS B3761 " (cutoff:3.500A) Processing helix chain 'B' and resid 3771 through 3785 Processing helix chain 'B' and resid 3788 through 3801 removed outlier: 4.126A pdb=" N SER B3800 " --> pdb=" O GLY B3796 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS B3801 " --> pdb=" O LEU B3797 " (cutoff:3.500A) Processing helix chain 'B' and resid 3806 through 3815 Processing helix chain 'B' and resid 3834 through 3846 Processing helix chain 'B' and resid 3852 through 3861 Processing helix chain 'B' and resid 3870 through 3894 removed outlier: 3.628A pdb=" N SER B3874 " --> pdb=" O ASN B3870 " (cutoff:3.500A) Processing helix chain 'B' and resid 3900 through 3926 removed outlier: 3.651A pdb=" N LYS B3909 " --> pdb=" O ARG B3905 " (cutoff:3.500A) Processing helix chain 'B' and resid 3929 through 3939 Processing helix chain 'B' and resid 3941 through 3962 removed outlier: 4.029A pdb=" N MET B3957 " --> pdb=" O ALA B3953 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS B3958 " --> pdb=" O HIS B3954 " (cutoff:3.500A) Processing helix chain 'B' and resid 3965 through 3987 Processing helix chain 'B' and resid 3994 through 4008 Processing helix chain 'B' and resid 4009 through 4028 removed outlier: 4.168A pdb=" N MET B4013 " --> pdb=" O ASN B4009 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B4024 " --> pdb=" O MET B4020 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B4025 " --> pdb=" O PHE B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4045 through 4056 Processing helix chain 'B' and resid 4060 through 4071 Processing helix chain 'B' and resid 4085 through 4110 Proline residue: B4091 - end of helix Processing helix chain 'B' and resid 4113 through 4123 Processing helix chain 'B' and resid 4123 through 4131 removed outlier: 3.544A pdb=" N LEU B4127 " --> pdb=" O ALA B4123 " (cutoff:3.500A) Processing helix chain 'B' and resid 4155 through 4162 Processing helix chain 'B' and resid 4163 through 4179 removed outlier: 3.704A pdb=" N LYS B4167 " --> pdb=" O LYS B4163 " (cutoff:3.500A) Processing helix chain 'B' and resid 4185 through 4207 Processing helix chain 'B' and resid 4487 through 4499 Processing helix chain 'B' and resid 4499 through 4518 removed outlier: 4.049A pdb=" N MET B4503 " --> pdb=" O ASN B4499 " (cutoff:3.500A) Processing helix chain 'B' and resid 4568 through 4594 Processing helix chain 'B' and resid 4595 through 4613 Processing helix chain 'B' and resid 4629 through 4631 No H-bonds generated for 'chain 'B' and resid 4629 through 4631' Processing helix chain 'B' and resid 4632 through 4637 removed outlier: 3.926A pdb=" N ILE B4636 " --> pdb=" O ASP B4632 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B4637 " --> pdb=" O ARG B4633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4632 through 4637' Processing helix chain 'B' and resid 4642 through 4646 removed outlier: 3.873A pdb=" N TYR B4645 " --> pdb=" O PRO B4642 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4663 removed outlier: 3.877A pdb=" N ARG B4652 " --> pdb=" O LYS B4648 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B4658 " --> pdb=" O VAL B4654 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B4659 " --> pdb=" O MET B4655 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU B4660 " --> pdb=" O ASP B4656 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE B4661 " --> pdb=" O LYS B4657 " (cutoff:3.500A) Processing helix chain 'B' and resid 4663 through 4672 Processing helix chain 'B' and resid 4703 through 4715 Processing helix chain 'B' and resid 4717 through 4736 Processing helix chain 'B' and resid 4738 through 4744 removed outlier: 4.177A pdb=" N ALA B4741 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS B4743 " --> pdb=" O PHE B4740 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B4744 " --> pdb=" O ALA B4741 " (cutoff:3.500A) Processing helix chain 'B' and resid 4745 through 4749 Processing helix chain 'B' and resid 4751 through 4763 removed outlier: 4.180A pdb=" N ARG B4755 " --> pdb=" O PHE B4751 " (cutoff:3.500A) Processing helix chain 'B' and resid 4764 through 4789 removed outlier: 3.524A pdb=" N PHE B4789 " --> pdb=" O VAL B4785 " (cutoff:3.500A) Processing helix chain 'B' and resid 4809 through 4823 removed outlier: 3.741A pdb=" N ARG B4823 " --> pdb=" O TYR B4819 " (cutoff:3.500A) Processing helix chain 'B' and resid 4838 through 4885 removed outlier: 3.741A pdb=" N TYR B4843 " --> pdb=" O GLU B4839 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B4857 " --> pdb=" O PHE B4853 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE B4858 " --> pdb=" O PHE B4854 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B4865 " --> pdb=" O ALA B4861 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B4866 " --> pdb=" O ILE B4862 " (cutoff:3.500A) Processing helix chain 'B' and resid 4904 through 4914 removed outlier: 3.563A pdb=" N THR B4908 " --> pdb=" O HIS B4904 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS B4914 " --> pdb=" O THR B4910 " (cutoff:3.500A) Processing helix chain 'B' and resid 4916 through 4929 removed outlier: 3.841A pdb=" N LEU B4920 " --> pdb=" O LEU B4916 " (cutoff:3.500A) Processing helix chain 'B' and resid 4935 through 4948 Processing helix chain 'B' and resid 4958 through 4963 removed outlier: 4.024A pdb=" N TYR B4963 " --> pdb=" O PHE B4959 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 66 removed outlier: 3.985A pdb=" N GLY C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 63 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.923A pdb=" N ALA D 105 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN D 106 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 409 through 439 removed outlier: 4.298A pdb=" N VAL D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 420 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 428 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.638A pdb=" N PHE D 489 " --> pdb=" O ARG D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 506 removed outlier: 4.106A pdb=" N LEU D 497 " --> pdb=" O GLY D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 540 removed outlier: 3.524A pdb=" N LEU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 removed outlier: 4.028A pdb=" N CYS D 548 " --> pdb=" O ASN D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 553 No H-bonds generated for 'chain 'D' and resid 551 through 553' Processing helix chain 'D' and resid 554 through 563 removed outlier: 4.108A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 582 removed outlier: 3.696A pdb=" N ILE D 571 " --> pdb=" O ALA D 567 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 581 " --> pdb=" O CYS D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.654A pdb=" N ILE D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.577A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 619 removed outlier: 3.614A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 638 through 640 No H-bonds generated for 'chain 'D' and resid 638 through 640' Processing helix chain 'D' and resid 821 through 826 removed outlier: 3.504A pdb=" N VAL D 826 " --> pdb=" O TYR D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 900 Processing helix chain 'D' and resid 929 through 946 removed outlier: 3.996A pdb=" N MET D 935 " --> pdb=" O TYR D 931 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 940 " --> pdb=" O SER D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1011 removed outlier: 3.622A pdb=" N GLU D 993 " --> pdb=" O THR D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1059 removed outlier: 4.226A pdb=" N ASN D1046 " --> pdb=" O THR D1042 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU D1050 " --> pdb=" O ASN D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1091 through 1095 removed outlier: 3.626A pdb=" N ALA D1095 " --> pdb=" O LYS D1092 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1224 Processing helix chain 'D' and resid 1570 through 1576 removed outlier: 3.526A pdb=" N GLU D1574 " --> pdb=" O LEU D1570 " (cutoff:3.500A) Processing helix chain 'D' and resid 1643 through 1646 Processing helix chain 'D' and resid 1647 through 1665 Processing helix chain 'D' and resid 1669 through 1681 removed outlier: 3.607A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP D1681 " --> pdb=" O CYS D1677 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 removed outlier: 3.707A pdb=" N GLU D1690 " --> pdb=" O LEU D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1695 through 1711 removed outlier: 3.750A pdb=" N ILE D1707 " --> pdb=" O TYR D1703 " (cutoff:3.500A) Processing helix chain 'D' and resid 1711 through 1722 Processing helix chain 'D' and resid 1730 through 1735 Processing helix chain 'D' and resid 1783 through 1803 removed outlier: 3.972A pdb=" N ALA D1789 " --> pdb=" O ASP D1785 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1831 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1900 through 1947 removed outlier: 3.562A pdb=" N LYS D1904 " --> pdb=" O PRO D1900 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU D1909 " --> pdb=" O LEU D1905 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D1910 " --> pdb=" O GLN D1906 " (cutoff:3.500A) Processing helix chain 'D' and resid 1999 through 2012 Processing helix chain 'D' and resid 2024 through 2039 removed outlier: 4.128A pdb=" N TYR D2039 " --> pdb=" O GLU D2035 " (cutoff:3.500A) Processing helix chain 'D' and resid 2059 through 2074 removed outlier: 3.633A pdb=" N GLU D2073 " --> pdb=" O ARG D2069 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER D2074 " --> pdb=" O TRP D2070 " (cutoff:3.500A) Processing helix chain 'D' and resid 2078 through 2093 removed outlier: 3.521A pdb=" N VAL D2082 " --> pdb=" O ASP D2078 " (cutoff:3.500A) Processing helix chain 'D' and resid 2096 through 2106 removed outlier: 3.814A pdb=" N ALA D2102 " --> pdb=" O GLY D2098 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU D2103 " --> pdb=" O LEU D2099 " (cutoff:3.500A) Proline residue: D2104 - end of helix Processing helix chain 'D' and resid 2113 through 2132 removed outlier: 3.669A pdb=" N THR D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) Processing helix chain 'D' and resid 2139 through 2151 Processing helix chain 'D' and resid 2160 through 2167 removed outlier: 3.907A pdb=" N ARG D2164 " --> pdb=" O PRO D2160 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2180 Processing helix chain 'D' and resid 2192 through 2206 removed outlier: 3.622A pdb=" N PHE D2200 " --> pdb=" O ASN D2196 " (cutoff:3.500A) Processing helix chain 'D' and resid 2208 through 2216 removed outlier: 3.555A pdb=" N MET D2215 " --> pdb=" O ASN D2211 " (cutoff:3.500A) Processing helix chain 'D' and resid 2218 through 2223 Processing helix chain 'D' and resid 2239 through 2247 removed outlier: 3.538A pdb=" N SER D2247 " --> pdb=" O VAL D2243 " (cutoff:3.500A) Processing helix chain 'D' and resid 2251 through 2258 Processing helix chain 'D' and resid 2259 through 2269 removed outlier: 4.067A pdb=" N LEU D2263 " --> pdb=" O ARG D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2295 through 2308 removed outlier: 3.660A pdb=" N TYR D2299 " --> pdb=" O GLU D2295 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) Processing helix chain 'D' and resid 2315 through 2328 Processing helix chain 'D' and resid 2344 through 2349 removed outlier: 3.602A pdb=" N GLU D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) Processing helix chain 'D' and resid 2387 through 2401 Processing helix chain 'D' and resid 2417 through 2426 removed outlier: 4.317A pdb=" N ILE D2423 " --> pdb=" O ARG D2419 " (cutoff:3.500A) Processing helix chain 'D' and resid 2432 through 2442 removed outlier: 4.043A pdb=" N PHE D2441 " --> pdb=" O ILE D2437 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN D2442 " --> pdb=" O SER D2438 " (cutoff:3.500A) Processing helix chain 'D' and resid 2462 through 2477 removed outlier: 3.845A pdb=" N LYS D2466 " --> pdb=" O CYS D2462 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D2467 " --> pdb=" O PRO D2463 " (cutoff:3.500A) Processing helix chain 'D' and resid 2482 through 2487 Processing helix chain 'D' and resid 2493 through 2499 Processing helix chain 'D' and resid 2500 through 2502 No H-bonds generated for 'chain 'D' and resid 2500 through 2502' Processing helix chain 'D' and resid 2512 through 2524 removed outlier: 3.930A pdb=" N ASN D2518 " --> pdb=" O ALA D2514 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D2521 " --> pdb=" O LEU D2517 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N CYS D2522 " --> pdb=" O ASN D2518 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR D2523 " --> pdb=" O ARG D2519 " (cutoff:3.500A) Processing helix chain 'D' and resid 2525 through 2529 removed outlier: 3.772A pdb=" N LEU D2529 " --> pdb=" O LEU D2526 " (cutoff:3.500A) Processing helix chain 'D' and resid 2535 through 2553 removed outlier: 4.023A pdb=" N THR D2539 " --> pdb=" O LEU D2535 " (cutoff:3.500A) Processing helix chain 'D' and resid 2559 through 2575 removed outlier: 3.637A pdb=" N LYS D2564 " --> pdb=" O CYS D2560 " (cutoff:3.500A) Processing helix chain 'D' and resid 2583 through 2601 removed outlier: 3.701A pdb=" N ARG D2592 " --> pdb=" O HIS D2588 " (cutoff:3.500A) Proline residue: D2598 - end of helix Processing helix chain 'D' and resid 2606 through 2622 removed outlier: 3.584A pdb=" N ARG D2617 " --> pdb=" O ASN D2613 " (cutoff:3.500A) Processing helix chain 'D' and resid 2635 through 2650 Processing helix chain 'D' and resid 2651 through 2653 No H-bonds generated for 'chain 'D' and resid 2651 through 2653' Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2668 - end of helix Processing helix chain 'D' and resid 2715 through 2740 removed outlier: 3.588A pdb=" N GLU D2719 " --> pdb=" O PRO D2715 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE D2721 " --> pdb=" O LYS D2717 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS D2724 " --> pdb=" O TYR D2720 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU D2727 " --> pdb=" O ASN D2723 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2786 removed outlier: 4.644A pdb=" N TYR D2772 " --> pdb=" O GLU D2768 " (cutoff:3.500A) Proline residue: D2775 - end of helix Processing helix chain 'D' and resid 2835 through 2865 removed outlier: 3.845A pdb=" N GLU D2860 " --> pdb=" O LYS D2856 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D2862 " --> pdb=" O LYS D2858 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER D2863 " --> pdb=" O LEU D2859 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D2864 " --> pdb=" O GLU D2860 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY D2865 " --> pdb=" O LEU D2861 " (cutoff:3.500A) Processing helix chain 'D' and resid 2880 through 2900 removed outlier: 4.115A pdb=" N ASP D2886 " --> pdb=" O GLU D2882 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS D2889 " --> pdb=" O LYS D2885 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D2894 " --> pdb=" O ALA D2890 " (cutoff:3.500A) Processing helix chain 'D' and resid 2983 through 3003 Proline residue: D2990 - end of helix Processing helix chain 'D' and resid 3010 through 3027 Processing helix chain 'D' and resid 3035 through 3049 Processing helix chain 'D' and resid 3051 through 3055 removed outlier: 3.839A pdb=" N VAL D3054 " --> pdb=" O LEU D3051 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D3055 " --> pdb=" O GLU D3052 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3051 through 3055' Processing helix chain 'D' and resid 3062 through 3079 Processing helix chain 'D' and resid 3101 through 3117 removed outlier: 3.784A pdb=" N MET D3105 " --> pdb=" O ALA D3101 " (cutoff:3.500A) Processing helix chain 'D' and resid 3125 through 3144 Processing helix chain 'D' and resid 3150 through 3164 Processing helix chain 'D' and resid 3171 through 3181 Processing helix chain 'D' and resid 3614 through 3629 Processing helix chain 'D' and resid 3637 through 3646 Processing helix chain 'D' and resid 3663 through 3677 Processing helix chain 'D' and resid 3686 through 3698 Processing helix chain 'D' and resid 3715 through 3734 Processing helix chain 'D' and resid 3736 through 3748 removed outlier: 3.657A pdb=" N MET D3740 " --> pdb=" O GLY D3736 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) Processing helix chain 'D' and resid 3753 through 3767 removed outlier: 3.679A pdb=" N ALA D3765 " --> pdb=" O LYS D3761 " (cutoff:3.500A) Processing helix chain 'D' and resid 3771 through 3785 Processing helix chain 'D' and resid 3788 through 3801 removed outlier: 4.126A pdb=" N SER D3800 " --> pdb=" O GLY D3796 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS D3801 " --> pdb=" O LEU D3797 " (cutoff:3.500A) Processing helix chain 'D' and resid 3806 through 3815 Processing helix chain 'D' and resid 3834 through 3846 Processing helix chain 'D' and resid 3852 through 3861 Processing helix chain 'D' and resid 3870 through 3894 removed outlier: 3.628A pdb=" N SER D3874 " --> pdb=" O ASN D3870 " (cutoff:3.500A) Processing helix chain 'D' and resid 3900 through 3926 removed outlier: 3.651A pdb=" N LYS D3909 " --> pdb=" O ARG D3905 " (cutoff:3.500A) Processing helix chain 'D' and resid 3929 through 3939 Processing helix chain 'D' and resid 3941 through 3962 removed outlier: 4.029A pdb=" N MET D3957 " --> pdb=" O ALA D3953 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS D3958 " --> pdb=" O HIS D3954 " (cutoff:3.500A) Processing helix chain 'D' and resid 3965 through 3987 Processing helix chain 'D' and resid 3994 through 4008 Processing helix chain 'D' and resid 4009 through 4028 removed outlier: 4.168A pdb=" N MET D4013 " --> pdb=" O ASN D4009 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU D4024 " --> pdb=" O MET D4020 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D4025 " --> pdb=" O PHE D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4045 through 4056 Processing helix chain 'D' and resid 4060 through 4071 Processing helix chain 'D' and resid 4085 through 4110 Proline residue: D4091 - end of helix Processing helix chain 'D' and resid 4113 through 4123 Processing helix chain 'D' and resid 4123 through 4131 removed outlier: 3.544A pdb=" N LEU D4127 " --> pdb=" O ALA D4123 " (cutoff:3.500A) Processing helix chain 'D' and resid 4155 through 4162 Processing helix chain 'D' and resid 4163 through 4179 removed outlier: 3.705A pdb=" N LYS D4167 " --> pdb=" O LYS D4163 " (cutoff:3.500A) Processing helix chain 'D' and resid 4185 through 4207 Processing helix chain 'D' and resid 4487 through 4499 Processing helix chain 'D' and resid 4499 through 4518 removed outlier: 4.049A pdb=" N MET D4503 " --> pdb=" O ASN D4499 " (cutoff:3.500A) Processing helix chain 'D' and resid 4568 through 4594 Processing helix chain 'D' and resid 4595 through 4613 Processing helix chain 'D' and resid 4629 through 4631 No H-bonds generated for 'chain 'D' and resid 4629 through 4631' Processing helix chain 'D' and resid 4632 through 4637 removed outlier: 3.926A pdb=" N ILE D4636 " --> pdb=" O ASP D4632 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN D4637 " --> pdb=" O ARG D4633 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4632 through 4637' Processing helix chain 'D' and resid 4642 through 4646 removed outlier: 3.873A pdb=" N TYR D4645 " --> pdb=" O PRO D4642 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4663 removed outlier: 3.877A pdb=" N ARG D4652 " --> pdb=" O LYS D4648 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR D4658 " --> pdb=" O VAL D4654 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY D4659 " --> pdb=" O MET D4655 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU D4660 " --> pdb=" O ASP D4656 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE D4661 " --> pdb=" O LYS D4657 " (cutoff:3.500A) Processing helix chain 'D' and resid 4663 through 4672 Processing helix chain 'D' and resid 4703 through 4715 Processing helix chain 'D' and resid 4717 through 4736 Processing helix chain 'D' and resid 4738 through 4744 removed outlier: 4.177A pdb=" N ALA D4741 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS D4743 " --> pdb=" O PHE D4740 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU D4744 " --> pdb=" O ALA D4741 " (cutoff:3.500A) Processing helix chain 'D' and resid 4745 through 4749 Processing helix chain 'D' and resid 4751 through 4763 removed outlier: 4.180A pdb=" N ARG D4755 " --> pdb=" O PHE D4751 " (cutoff:3.500A) Processing helix chain 'D' and resid 4764 through 4789 removed outlier: 3.524A pdb=" N PHE D4789 " --> pdb=" O VAL D4785 " (cutoff:3.500A) Processing helix chain 'D' and resid 4809 through 4823 removed outlier: 3.740A pdb=" N ARG D4823 " --> pdb=" O TYR D4819 " (cutoff:3.500A) Processing helix chain 'D' and resid 4838 through 4885 removed outlier: 3.741A pdb=" N TYR D4843 " --> pdb=" O GLU D4839 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D4857 " --> pdb=" O PHE D4853 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE D4858 " --> pdb=" O PHE D4854 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY D4865 " --> pdb=" O ALA D4861 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU D4866 " --> pdb=" O ILE D4862 " (cutoff:3.500A) Processing helix chain 'D' and resid 4904 through 4914 removed outlier: 3.577A pdb=" N THR D4908 " --> pdb=" O HIS D4904 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS D4914 " --> pdb=" O THR D4910 " (cutoff:3.500A) Processing helix chain 'D' and resid 4916 through 4929 removed outlier: 3.841A pdb=" N LEU D4920 " --> pdb=" O LEU D4916 " (cutoff:3.500A) Processing helix chain 'D' and resid 4935 through 4948 Processing helix chain 'D' and resid 4958 through 4963 removed outlier: 4.023A pdb=" N TYR D4963 " --> pdb=" O PHE D4959 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 66 removed outlier: 3.984A pdb=" N GLY E 62 " --> pdb=" O GLY E 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 63 " --> pdb=" O PHE E 59 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 84 Processing helix chain 'F' and resid 101 through 106 removed outlier: 3.923A pdb=" N ALA F 105 " --> pdb=" O MET F 102 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN F 106 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 327 Processing helix chain 'F' and resid 409 through 439 removed outlier: 4.298A pdb=" N VAL F 418 " --> pdb=" O ARG F 414 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG F 428 " --> pdb=" O PHE F 424 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 438 " --> pdb=" O ASP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 463 Processing helix chain 'F' and resid 471 through 491 removed outlier: 3.638A pdb=" N PHE F 489 " --> pdb=" O ARG F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 506 removed outlier: 4.106A pdb=" N LEU F 497 " --> pdb=" O GLY F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 540 removed outlier: 3.525A pdb=" N LEU F 540 " --> pdb=" O LEU F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 550 removed outlier: 4.028A pdb=" N CYS F 548 " --> pdb=" O ASN F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 553 No H-bonds generated for 'chain 'F' and resid 551 through 553' Processing helix chain 'F' and resid 554 through 563 removed outlier: 4.107A pdb=" N GLU F 563 " --> pdb=" O ILE F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 582 removed outlier: 3.697A pdb=" N ILE F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F 581 " --> pdb=" O CYS F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 589 removed outlier: 3.653A pdb=" N ILE F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 604 removed outlier: 3.578A pdb=" N LEU F 601 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP F 602 " --> pdb=" O ILE F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 619 removed outlier: 3.614A pdb=" N LEU F 611 " --> pdb=" O ASN F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 637 Processing helix chain 'F' and resid 638 through 640 No H-bonds generated for 'chain 'F' and resid 638 through 640' Processing helix chain 'F' and resid 821 through 826 removed outlier: 3.503A pdb=" N VAL F 826 " --> pdb=" O TYR F 823 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 900 Processing helix chain 'F' and resid 929 through 946 removed outlier: 3.997A pdb=" N MET F 935 " --> pdb=" O TYR F 931 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 940 " --> pdb=" O SER F 936 " (cutoff:3.500A) Processing helix chain 'F' and resid 989 through 1011 removed outlier: 3.622A pdb=" N GLU F 993 " --> pdb=" O THR F 989 " (cutoff:3.500A) Processing helix chain 'F' and resid 1042 through 1059 removed outlier: 4.227A pdb=" N ASN F1046 " --> pdb=" O THR F1042 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU F1050 " --> pdb=" O ASN F1046 " (cutoff:3.500A) Processing helix chain 'F' and resid 1091 through 1095 removed outlier: 3.626A pdb=" N ALA F1095 " --> pdb=" O LYS F1092 " (cutoff:3.500A) Processing helix chain 'F' and resid 1220 through 1224 Processing helix chain 'F' and resid 1570 through 1576 removed outlier: 3.527A pdb=" N GLU F1574 " --> pdb=" O LEU F1570 " (cutoff:3.500A) Processing helix chain 'F' and resid 1643 through 1646 Processing helix chain 'F' and resid 1647 through 1665 Processing helix chain 'F' and resid 1669 through 1681 removed outlier: 3.606A pdb=" N SER F1678 " --> pdb=" O HIS F1674 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP F1681 " --> pdb=" O CYS F1677 " (cutoff:3.500A) Processing helix chain 'F' and resid 1681 through 1691 removed outlier: 3.706A pdb=" N GLU F1690 " --> pdb=" O LEU F1686 " (cutoff:3.500A) Processing helix chain 'F' and resid 1695 through 1711 removed outlier: 3.750A pdb=" N ILE F1707 " --> pdb=" O TYR F1703 " (cutoff:3.500A) Processing helix chain 'F' and resid 1711 through 1722 Processing helix chain 'F' and resid 1730 through 1735 Processing helix chain 'F' and resid 1783 through 1803 removed outlier: 3.972A pdb=" N ALA F1789 " --> pdb=" O ASP F1785 " (cutoff:3.500A) Processing helix chain 'F' and resid 1813 through 1831 Proline residue: F1820 - end of helix Processing helix chain 'F' and resid 1836 through 1847 Processing helix chain 'F' and resid 1900 through 1947 removed outlier: 3.562A pdb=" N LYS F1904 " --> pdb=" O PRO F1900 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU F1909 " --> pdb=" O LEU F1905 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F1910 " --> pdb=" O GLN F1906 " (cutoff:3.500A) Processing helix chain 'F' and resid 1999 through 2012 Processing helix chain 'F' and resid 2024 through 2039 removed outlier: 4.128A pdb=" N TYR F2039 " --> pdb=" O GLU F2035 " (cutoff:3.500A) Processing helix chain 'F' and resid 2059 through 2074 removed outlier: 3.634A pdb=" N GLU F2073 " --> pdb=" O ARG F2069 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER F2074 " --> pdb=" O TRP F2070 " (cutoff:3.500A) Processing helix chain 'F' and resid 2078 through 2093 removed outlier: 3.521A pdb=" N VAL F2082 " --> pdb=" O ASP F2078 " (cutoff:3.500A) Processing helix chain 'F' and resid 2096 through 2106 removed outlier: 3.815A pdb=" N ALA F2102 " --> pdb=" O GLY F2098 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU F2103 " --> pdb=" O LEU F2099 " (cutoff:3.500A) Proline residue: F2104 - end of helix Processing helix chain 'F' and resid 2113 through 2132 removed outlier: 3.669A pdb=" N THR F2117 " --> pdb=" O SER F2113 " (cutoff:3.500A) Processing helix chain 'F' and resid 2139 through 2151 Processing helix chain 'F' and resid 2160 through 2167 removed outlier: 3.907A pdb=" N ARG F2164 " --> pdb=" O PRO F2160 " (cutoff:3.500A) Processing helix chain 'F' and resid 2167 through 2180 Processing helix chain 'F' and resid 2192 through 2206 removed outlier: 3.622A pdb=" N PHE F2200 " --> pdb=" O ASN F2196 " (cutoff:3.500A) Processing helix chain 'F' and resid 2208 through 2216 removed outlier: 3.555A pdb=" N MET F2215 " --> pdb=" O ASN F2211 " (cutoff:3.500A) Processing helix chain 'F' and resid 2218 through 2223 Processing helix chain 'F' and resid 2239 through 2247 removed outlier: 3.537A pdb=" N SER F2247 " --> pdb=" O VAL F2243 " (cutoff:3.500A) Processing helix chain 'F' and resid 2251 through 2258 Processing helix chain 'F' and resid 2259 through 2269 removed outlier: 4.067A pdb=" N LEU F2263 " --> pdb=" O ARG F2259 " (cutoff:3.500A) Processing helix chain 'F' and resid 2295 through 2308 removed outlier: 3.661A pdb=" N TYR F2299 " --> pdb=" O GLU F2295 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE F2308 " --> pdb=" O ARG F2304 " (cutoff:3.500A) Processing helix chain 'F' and resid 2315 through 2328 Processing helix chain 'F' and resid 2344 through 2349 removed outlier: 3.601A pdb=" N GLU F2349 " --> pdb=" O LEU F2345 " (cutoff:3.500A) Processing helix chain 'F' and resid 2387 through 2401 Processing helix chain 'F' and resid 2417 through 2426 removed outlier: 4.318A pdb=" N ILE F2423 " --> pdb=" O ARG F2419 " (cutoff:3.500A) Processing helix chain 'F' and resid 2432 through 2442 removed outlier: 4.042A pdb=" N PHE F2441 " --> pdb=" O ILE F2437 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN F2442 " --> pdb=" O SER F2438 " (cutoff:3.500A) Processing helix chain 'F' and resid 2462 through 2477 removed outlier: 3.844A pdb=" N LYS F2466 " --> pdb=" O CYS F2462 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA F2467 " --> pdb=" O PRO F2463 " (cutoff:3.500A) Processing helix chain 'F' and resid 2482 through 2487 Processing helix chain 'F' and resid 2493 through 2499 Processing helix chain 'F' and resid 2500 through 2502 No H-bonds generated for 'chain 'F' and resid 2500 through 2502' Processing helix chain 'F' and resid 2512 through 2524 removed outlier: 3.929A pdb=" N ASN F2518 " --> pdb=" O ALA F2514 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU F2521 " --> pdb=" O LEU F2517 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N CYS F2522 " --> pdb=" O ASN F2518 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR F2523 " --> pdb=" O ARG F2519 " (cutoff:3.500A) Processing helix chain 'F' and resid 2525 through 2529 removed outlier: 3.772A pdb=" N LEU F2529 " --> pdb=" O LEU F2526 " (cutoff:3.500A) Processing helix chain 'F' and resid 2535 through 2553 removed outlier: 4.023A pdb=" N THR F2539 " --> pdb=" O LEU F2535 " (cutoff:3.500A) Processing helix chain 'F' and resid 2559 through 2575 removed outlier: 3.637A pdb=" N LYS F2564 " --> pdb=" O CYS F2560 " (cutoff:3.500A) Processing helix chain 'F' and resid 2583 through 2601 removed outlier: 3.701A pdb=" N ARG F2592 " --> pdb=" O HIS F2588 " (cutoff:3.500A) Proline residue: F2598 - end of helix Processing helix chain 'F' and resid 2606 through 2622 removed outlier: 3.583A pdb=" N ARG F2617 " --> pdb=" O ASN F2613 " (cutoff:3.500A) Processing helix chain 'F' and resid 2635 through 2650 Processing helix chain 'F' and resid 2651 through 2653 No H-bonds generated for 'chain 'F' and resid 2651 through 2653' Processing helix chain 'F' and resid 2659 through 2677 Proline residue: F2668 - end of helix Processing helix chain 'F' and resid 2715 through 2740 removed outlier: 3.588A pdb=" N GLU F2719 " --> pdb=" O PRO F2715 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE F2721 " --> pdb=" O LYS F2717 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS F2724 " --> pdb=" O TYR F2720 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU F2727 " --> pdb=" O ASN F2723 " (cutoff:3.500A) Processing helix chain 'F' and resid 2765 through 2786 removed outlier: 4.644A pdb=" N TYR F2772 " --> pdb=" O GLU F2768 " (cutoff:3.500A) Proline residue: F2775 - end of helix Processing helix chain 'F' and resid 2835 through 2865 removed outlier: 3.844A pdb=" N GLU F2860 " --> pdb=" O LYS F2856 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F2862 " --> pdb=" O LYS F2858 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER F2863 " --> pdb=" O LEU F2859 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS F2864 " --> pdb=" O GLU F2860 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY F2865 " --> pdb=" O LEU F2861 " (cutoff:3.500A) Processing helix chain 'F' and resid 2880 through 2900 removed outlier: 4.115A pdb=" N ASP F2886 " --> pdb=" O GLU F2882 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS F2889 " --> pdb=" O LYS F2885 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F2893 " --> pdb=" O LYS F2889 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F2894 " --> pdb=" O ALA F2890 " (cutoff:3.500A) Processing helix chain 'F' and resid 2983 through 3003 Proline residue: F2990 - end of helix Processing helix chain 'F' and resid 3010 through 3027 Processing helix chain 'F' and resid 3035 through 3049 Processing helix chain 'F' and resid 3051 through 3055 removed outlier: 3.839A pdb=" N VAL F3054 " --> pdb=" O LEU F3051 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS F3055 " --> pdb=" O GLU F3052 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3051 through 3055' Processing helix chain 'F' and resid 3062 through 3079 Processing helix chain 'F' and resid 3101 through 3117 removed outlier: 3.785A pdb=" N MET F3105 " --> pdb=" O ALA F3101 " (cutoff:3.500A) Processing helix chain 'F' and resid 3125 through 3144 Processing helix chain 'F' and resid 3150 through 3164 Processing helix chain 'F' and resid 3171 through 3181 Processing helix chain 'F' and resid 3614 through 3629 Processing helix chain 'F' and resid 3637 through 3646 Processing helix chain 'F' and resid 3663 through 3677 Processing helix chain 'F' and resid 3686 through 3698 Processing helix chain 'F' and resid 3715 through 3734 Processing helix chain 'F' and resid 3736 through 3748 removed outlier: 3.656A pdb=" N MET F3740 " --> pdb=" O GLY F3736 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F3741 " --> pdb=" O ALA F3737 " (cutoff:3.500A) Processing helix chain 'F' and resid 3753 through 3767 removed outlier: 3.679A pdb=" N ALA F3765 " --> pdb=" O LYS F3761 " (cutoff:3.500A) Processing helix chain 'F' and resid 3771 through 3785 Processing helix chain 'F' and resid 3788 through 3801 removed outlier: 4.125A pdb=" N SER F3800 " --> pdb=" O GLY F3796 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS F3801 " --> pdb=" O LEU F3797 " (cutoff:3.500A) Processing helix chain 'F' and resid 3806 through 3815 Processing helix chain 'F' and resid 3834 through 3846 Processing helix chain 'F' and resid 3852 through 3861 Processing helix chain 'F' and resid 3870 through 3894 removed outlier: 3.628A pdb=" N SER F3874 " --> pdb=" O ASN F3870 " (cutoff:3.500A) Processing helix chain 'F' and resid 3900 through 3926 removed outlier: 3.651A pdb=" N LYS F3909 " --> pdb=" O ARG F3905 " (cutoff:3.500A) Processing helix chain 'F' and resid 3929 through 3939 Processing helix chain 'F' and resid 3941 through 3962 removed outlier: 4.029A pdb=" N MET F3957 " --> pdb=" O ALA F3953 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS F3958 " --> pdb=" O HIS F3954 " (cutoff:3.500A) Processing helix chain 'F' and resid 3965 through 3987 Processing helix chain 'F' and resid 3994 through 4008 Processing helix chain 'F' and resid 4009 through 4028 removed outlier: 4.168A pdb=" N MET F4013 " --> pdb=" O ASN F4009 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU F4024 " --> pdb=" O MET F4020 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS F4025 " --> pdb=" O PHE F4021 " (cutoff:3.500A) Processing helix chain 'F' and resid 4045 through 4056 Processing helix chain 'F' and resid 4060 through 4071 Processing helix chain 'F' and resid 4085 through 4110 Proline residue: F4091 - end of helix Processing helix chain 'F' and resid 4113 through 4123 Processing helix chain 'F' and resid 4123 through 4131 removed outlier: 3.545A pdb=" N LEU F4127 " --> pdb=" O ALA F4123 " (cutoff:3.500A) Processing helix chain 'F' and resid 4155 through 4162 Processing helix chain 'F' and resid 4163 through 4179 removed outlier: 3.704A pdb=" N LYS F4167 " --> pdb=" O LYS F4163 " (cutoff:3.500A) Processing helix chain 'F' and resid 4185 through 4207 Processing helix chain 'F' and resid 4487 through 4499 Processing helix chain 'F' and resid 4499 through 4518 removed outlier: 4.049A pdb=" N MET F4503 " --> pdb=" O ASN F4499 " (cutoff:3.500A) Processing helix chain 'F' and resid 4568 through 4594 Processing helix chain 'F' and resid 4595 through 4613 Processing helix chain 'F' and resid 4629 through 4631 No H-bonds generated for 'chain 'F' and resid 4629 through 4631' Processing helix chain 'F' and resid 4632 through 4637 removed outlier: 3.927A pdb=" N ILE F4636 " --> pdb=" O ASP F4632 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN F4637 " --> pdb=" O ARG F4633 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 4632 through 4637' Processing helix chain 'F' and resid 4642 through 4646 removed outlier: 3.873A pdb=" N TYR F4645 " --> pdb=" O PRO F4642 " (cutoff:3.500A) Processing helix chain 'F' and resid 4648 through 4663 removed outlier: 3.877A pdb=" N ARG F4652 " --> pdb=" O LYS F4648 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR F4658 " --> pdb=" O VAL F4654 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY F4659 " --> pdb=" O MET F4655 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU F4660 " --> pdb=" O ASP F4656 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE F4661 " --> pdb=" O LYS F4657 " (cutoff:3.500A) Processing helix chain 'F' and resid 4663 through 4672 Processing helix chain 'F' and resid 4703 through 4715 Processing helix chain 'F' and resid 4717 through 4736 Processing helix chain 'F' and resid 4738 through 4744 removed outlier: 4.177A pdb=" N ALA F4741 " --> pdb=" O PHE F4738 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS F4743 " --> pdb=" O PHE F4740 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F4744 " --> pdb=" O ALA F4741 " (cutoff:3.500A) Processing helix chain 'F' and resid 4745 through 4749 Processing helix chain 'F' and resid 4751 through 4763 removed outlier: 4.180A pdb=" N ARG F4755 " --> pdb=" O PHE F4751 " (cutoff:3.500A) Processing helix chain 'F' and resid 4764 through 4789 removed outlier: 3.524A pdb=" N PHE F4789 " --> pdb=" O VAL F4785 " (cutoff:3.500A) Processing helix chain 'F' and resid 4809 through 4823 removed outlier: 3.740A pdb=" N ARG F4823 " --> pdb=" O TYR F4819 " (cutoff:3.500A) Processing helix chain 'F' and resid 4838 through 4885 removed outlier: 3.741A pdb=" N TYR F4843 " --> pdb=" O GLU F4839 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F4857 " --> pdb=" O PHE F4853 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE F4858 " --> pdb=" O PHE F4854 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY F4865 " --> pdb=" O ALA F4861 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F4866 " --> pdb=" O ILE F4862 " (cutoff:3.500A) Processing helix chain 'F' and resid 4904 through 4914 removed outlier: 3.561A pdb=" N THR F4908 " --> pdb=" O HIS F4904 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS F4914 " --> pdb=" O THR F4910 " (cutoff:3.500A) Processing helix chain 'F' and resid 4916 through 4929 removed outlier: 3.841A pdb=" N LEU F4920 " --> pdb=" O LEU F4916 " (cutoff:3.500A) Processing helix chain 'F' and resid 4935 through 4948 Processing helix chain 'F' and resid 4958 through 4963 removed outlier: 4.024A pdb=" N TYR F4963 " --> pdb=" O PHE F4959 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.985A pdb=" N GLY G 62 " --> pdb=" O GLY G 58 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 63 " --> pdb=" O PHE G 59 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 84 Processing helix chain 'H' and resid 101 through 106 removed outlier: 3.922A pdb=" N ALA H 105 " --> pdb=" O MET H 102 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN H 106 " --> pdb=" O LYS H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 327 Processing helix chain 'H' and resid 409 through 439 removed outlier: 4.298A pdb=" N VAL H 418 " --> pdb=" O ARG H 414 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG H 420 " --> pdb=" O ALA H 416 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG H 428 " --> pdb=" O PHE H 424 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS H 438 " --> pdb=" O ASP H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 463 Processing helix chain 'H' and resid 471 through 491 removed outlier: 3.639A pdb=" N PHE H 489 " --> pdb=" O ARG H 485 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 506 removed outlier: 4.106A pdb=" N LEU H 497 " --> pdb=" O GLY H 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 525 through 540 removed outlier: 3.524A pdb=" N LEU H 540 " --> pdb=" O LEU H 536 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 550 removed outlier: 4.027A pdb=" N CYS H 548 " --> pdb=" O ASN H 544 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 553 No H-bonds generated for 'chain 'H' and resid 551 through 553' Processing helix chain 'H' and resid 554 through 563 removed outlier: 4.107A pdb=" N GLU H 563 " --> pdb=" O ILE H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 567 through 582 removed outlier: 3.697A pdb=" N ILE H 571 " --> pdb=" O ALA H 567 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU H 581 " --> pdb=" O CYS H 577 " (cutoff:3.500A) Processing helix chain 'H' and resid 584 through 589 removed outlier: 3.654A pdb=" N ILE H 588 " --> pdb=" O GLU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 590 through 604 removed outlier: 3.578A pdb=" N LEU H 601 " --> pdb=" O ILE H 597 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP H 602 " --> pdb=" O ILE H 598 " (cutoff:3.500A) Processing helix chain 'H' and resid 607 through 619 removed outlier: 3.614A pdb=" N LEU H 611 " --> pdb=" O ASN H 607 " (cutoff:3.500A) Processing helix chain 'H' and resid 625 through 637 Processing helix chain 'H' and resid 638 through 640 No H-bonds generated for 'chain 'H' and resid 638 through 640' Processing helix chain 'H' and resid 821 through 826 removed outlier: 3.502A pdb=" N VAL H 826 " --> pdb=" O TYR H 823 " (cutoff:3.500A) Processing helix chain 'H' and resid 878 through 900 Processing helix chain 'H' and resid 929 through 946 removed outlier: 3.996A pdb=" N MET H 935 " --> pdb=" O TYR H 931 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU H 940 " --> pdb=" O SER H 936 " (cutoff:3.500A) Processing helix chain 'H' and resid 989 through 1011 removed outlier: 3.621A pdb=" N GLU H 993 " --> pdb=" O THR H 989 " (cutoff:3.500A) Processing helix chain 'H' and resid 1042 through 1059 removed outlier: 4.227A pdb=" N ASN H1046 " --> pdb=" O THR H1042 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU H1050 " --> pdb=" O ASN H1046 " (cutoff:3.500A) Processing helix chain 'H' and resid 1091 through 1095 removed outlier: 3.626A pdb=" N ALA H1095 " --> pdb=" O LYS H1092 " (cutoff:3.500A) Processing helix chain 'H' and resid 1220 through 1224 Processing helix chain 'H' and resid 1570 through 1576 removed outlier: 3.527A pdb=" N GLU H1574 " --> pdb=" O LEU H1570 " (cutoff:3.500A) Processing helix chain 'H' and resid 1643 through 1646 Processing helix chain 'H' and resid 1647 through 1665 Processing helix chain 'H' and resid 1669 through 1681 removed outlier: 3.606A pdb=" N SER H1678 " --> pdb=" O HIS H1674 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP H1681 " --> pdb=" O CYS H1677 " (cutoff:3.500A) Processing helix chain 'H' and resid 1681 through 1691 removed outlier: 3.707A pdb=" N GLU H1690 " --> pdb=" O LEU H1686 " (cutoff:3.500A) Processing helix chain 'H' and resid 1695 through 1711 removed outlier: 3.750A pdb=" N ILE H1707 " --> pdb=" O TYR H1703 " (cutoff:3.500A) Processing helix chain 'H' and resid 1711 through 1722 Processing helix chain 'H' and resid 1730 through 1735 Processing helix chain 'H' and resid 1783 through 1803 removed outlier: 3.972A pdb=" N ALA H1789 " --> pdb=" O ASP H1785 " (cutoff:3.500A) Processing helix chain 'H' and resid 1813 through 1831 Proline residue: H1820 - end of helix Processing helix chain 'H' and resid 1836 through 1847 Processing helix chain 'H' and resid 1900 through 1947 removed outlier: 3.562A pdb=" N LYS H1904 " --> pdb=" O PRO H1900 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU H1909 " --> pdb=" O LEU H1905 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU H1910 " --> pdb=" O GLN H1906 " (cutoff:3.500A) Processing helix chain 'H' and resid 1999 through 2012 Processing helix chain 'H' and resid 2024 through 2039 removed outlier: 4.129A pdb=" N TYR H2039 " --> pdb=" O GLU H2035 " (cutoff:3.500A) Processing helix chain 'H' and resid 2059 through 2074 removed outlier: 3.634A pdb=" N GLU H2073 " --> pdb=" O ARG H2069 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER H2074 " --> pdb=" O TRP H2070 " (cutoff:3.500A) Processing helix chain 'H' and resid 2078 through 2093 removed outlier: 3.522A pdb=" N VAL H2082 " --> pdb=" O ASP H2078 " (cutoff:3.500A) Processing helix chain 'H' and resid 2096 through 2106 removed outlier: 3.814A pdb=" N ALA H2102 " --> pdb=" O GLY H2098 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU H2103 " --> pdb=" O LEU H2099 " (cutoff:3.500A) Proline residue: H2104 - end of helix Processing helix chain 'H' and resid 2113 through 2132 removed outlier: 3.670A pdb=" N THR H2117 " --> pdb=" O SER H2113 " (cutoff:3.500A) Processing helix chain 'H' and resid 2139 through 2151 Processing helix chain 'H' and resid 2160 through 2167 removed outlier: 3.907A pdb=" N ARG H2164 " --> pdb=" O PRO H2160 " (cutoff:3.500A) Processing helix chain 'H' and resid 2167 through 2180 Processing helix chain 'H' and resid 2192 through 2206 removed outlier: 3.622A pdb=" N PHE H2200 " --> pdb=" O ASN H2196 " (cutoff:3.500A) Processing helix chain 'H' and resid 2208 through 2216 removed outlier: 3.555A pdb=" N MET H2215 " --> pdb=" O ASN H2211 " (cutoff:3.500A) Processing helix chain 'H' and resid 2218 through 2223 Processing helix chain 'H' and resid 2239 through 2247 removed outlier: 3.537A pdb=" N SER H2247 " --> pdb=" O VAL H2243 " (cutoff:3.500A) Processing helix chain 'H' and resid 2251 through 2258 Processing helix chain 'H' and resid 2259 through 2269 removed outlier: 4.067A pdb=" N LEU H2263 " --> pdb=" O ARG H2259 " (cutoff:3.500A) Processing helix chain 'H' and resid 2295 through 2308 removed outlier: 3.660A pdb=" N TYR H2299 " --> pdb=" O GLU H2295 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE H2308 " --> pdb=" O ARG H2304 " (cutoff:3.500A) Processing helix chain 'H' and resid 2315 through 2328 Processing helix chain 'H' and resid 2344 through 2349 removed outlier: 3.602A pdb=" N GLU H2349 " --> pdb=" O LEU H2345 " (cutoff:3.500A) Processing helix chain 'H' and resid 2387 through 2401 Processing helix chain 'H' and resid 2417 through 2426 removed outlier: 4.317A pdb=" N ILE H2423 " --> pdb=" O ARG H2419 " (cutoff:3.500A) Processing helix chain 'H' and resid 2432 through 2442 removed outlier: 4.043A pdb=" N PHE H2441 " --> pdb=" O ILE H2437 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN H2442 " --> pdb=" O SER H2438 " (cutoff:3.500A) Processing helix chain 'H' and resid 2462 through 2477 removed outlier: 3.845A pdb=" N LYS H2466 " --> pdb=" O CYS H2462 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA H2467 " --> pdb=" O PRO H2463 " (cutoff:3.500A) Processing helix chain 'H' and resid 2482 through 2487 Processing helix chain 'H' and resid 2493 through 2499 Processing helix chain 'H' and resid 2500 through 2502 No H-bonds generated for 'chain 'H' and resid 2500 through 2502' Processing helix chain 'H' and resid 2512 through 2524 removed outlier: 3.930A pdb=" N ASN H2518 " --> pdb=" O ALA H2514 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU H2521 " --> pdb=" O LEU H2517 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N CYS H2522 " --> pdb=" O ASN H2518 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR H2523 " --> pdb=" O ARG H2519 " (cutoff:3.500A) Processing helix chain 'H' and resid 2525 through 2529 removed outlier: 3.772A pdb=" N LEU H2529 " --> pdb=" O LEU H2526 " (cutoff:3.500A) Processing helix chain 'H' and resid 2535 through 2553 removed outlier: 4.023A pdb=" N THR H2539 " --> pdb=" O LEU H2535 " (cutoff:3.500A) Processing helix chain 'H' and resid 2559 through 2575 removed outlier: 3.637A pdb=" N LYS H2564 " --> pdb=" O CYS H2560 " (cutoff:3.500A) Processing helix chain 'H' and resid 2583 through 2601 removed outlier: 3.700A pdb=" N ARG H2592 " --> pdb=" O HIS H2588 " (cutoff:3.500A) Proline residue: H2598 - end of helix Processing helix chain 'H' and resid 2606 through 2622 removed outlier: 3.583A pdb=" N ARG H2617 " --> pdb=" O ASN H2613 " (cutoff:3.500A) Processing helix chain 'H' and resid 2635 through 2650 Processing helix chain 'H' and resid 2651 through 2653 No H-bonds generated for 'chain 'H' and resid 2651 through 2653' Processing helix chain 'H' and resid 2659 through 2677 Proline residue: H2668 - end of helix Processing helix chain 'H' and resid 2715 through 2740 removed outlier: 3.586A pdb=" N GLU H2719 " --> pdb=" O PRO H2715 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE H2721 " --> pdb=" O LYS H2717 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS H2724 " --> pdb=" O TYR H2720 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU H2727 " --> pdb=" O ASN H2723 " (cutoff:3.500A) Processing helix chain 'H' and resid 2765 through 2786 removed outlier: 4.644A pdb=" N TYR H2772 " --> pdb=" O GLU H2768 " (cutoff:3.500A) Proline residue: H2775 - end of helix Processing helix chain 'H' and resid 2835 through 2865 removed outlier: 3.844A pdb=" N GLU H2860 " --> pdb=" O LYS H2856 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU H2862 " --> pdb=" O LYS H2858 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER H2863 " --> pdb=" O LEU H2859 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS H2864 " --> pdb=" O GLU H2860 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY H2865 " --> pdb=" O LEU H2861 " (cutoff:3.500A) Processing helix chain 'H' and resid 2880 through 2900 removed outlier: 4.115A pdb=" N ASP H2886 " --> pdb=" O GLU H2882 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS H2889 " --> pdb=" O LYS H2885 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE H2893 " --> pdb=" O LYS H2889 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU H2894 " --> pdb=" O ALA H2890 " (cutoff:3.500A) Processing helix chain 'H' and resid 2983 through 3003 Proline residue: H2990 - end of helix Processing helix chain 'H' and resid 3010 through 3027 Processing helix chain 'H' and resid 3035 through 3049 Processing helix chain 'H' and resid 3051 through 3055 removed outlier: 3.839A pdb=" N VAL H3054 " --> pdb=" O LEU H3051 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS H3055 " --> pdb=" O GLU H3052 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3051 through 3055' Processing helix chain 'H' and resid 3062 through 3079 Processing helix chain 'H' and resid 3101 through 3117 removed outlier: 3.784A pdb=" N MET H3105 " --> pdb=" O ALA H3101 " (cutoff:3.500A) Processing helix chain 'H' and resid 3125 through 3144 Processing helix chain 'H' and resid 3150 through 3164 Processing helix chain 'H' and resid 3171 through 3181 Processing helix chain 'H' and resid 3614 through 3629 Processing helix chain 'H' and resid 3637 through 3646 Processing helix chain 'H' and resid 3663 through 3677 Processing helix chain 'H' and resid 3686 through 3698 Processing helix chain 'H' and resid 3715 through 3734 Processing helix chain 'H' and resid 3736 through 3748 removed outlier: 3.656A pdb=" N MET H3740 " --> pdb=" O GLY H3736 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL H3741 " --> pdb=" O ALA H3737 " (cutoff:3.500A) Processing helix chain 'H' and resid 3753 through 3767 removed outlier: 3.678A pdb=" N ALA H3765 " --> pdb=" O LYS H3761 " (cutoff:3.500A) Processing helix chain 'H' and resid 3771 through 3785 Processing helix chain 'H' and resid 3788 through 3801 removed outlier: 4.126A pdb=" N SER H3800 " --> pdb=" O GLY H3796 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS H3801 " --> pdb=" O LEU H3797 " (cutoff:3.500A) Processing helix chain 'H' and resid 3806 through 3815 Processing helix chain 'H' and resid 3834 through 3846 Processing helix chain 'H' and resid 3852 through 3861 Processing helix chain 'H' and resid 3870 through 3894 removed outlier: 3.628A pdb=" N SER H3874 " --> pdb=" O ASN H3870 " (cutoff:3.500A) Processing helix chain 'H' and resid 3900 through 3926 removed outlier: 3.652A pdb=" N LYS H3909 " --> pdb=" O ARG H3905 " (cutoff:3.500A) Processing helix chain 'H' and resid 3929 through 3939 Processing helix chain 'H' and resid 3941 through 3962 removed outlier: 4.029A pdb=" N MET H3957 " --> pdb=" O ALA H3953 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYS H3958 " --> pdb=" O HIS H3954 " (cutoff:3.500A) Processing helix chain 'H' and resid 3965 through 3987 Processing helix chain 'H' and resid 3994 through 4008 Processing helix chain 'H' and resid 4009 through 4028 removed outlier: 4.169A pdb=" N MET H4013 " --> pdb=" O ASN H4009 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU H4024 " --> pdb=" O MET H4020 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS H4025 " --> pdb=" O PHE H4021 " (cutoff:3.500A) Processing helix chain 'H' and resid 4045 through 4056 Processing helix chain 'H' and resid 4060 through 4071 Processing helix chain 'H' and resid 4085 through 4110 Proline residue: H4091 - end of helix Processing helix chain 'H' and resid 4113 through 4123 Processing helix chain 'H' and resid 4123 through 4131 removed outlier: 3.544A pdb=" N LEU H4127 " --> pdb=" O ALA H4123 " (cutoff:3.500A) Processing helix chain 'H' and resid 4155 through 4162 Processing helix chain 'H' and resid 4163 through 4179 removed outlier: 3.704A pdb=" N LYS H4167 " --> pdb=" O LYS H4163 " (cutoff:3.500A) Processing helix chain 'H' and resid 4185 through 4207 Processing helix chain 'H' and resid 4487 through 4499 Processing helix chain 'H' and resid 4499 through 4518 removed outlier: 4.048A pdb=" N MET H4503 " --> pdb=" O ASN H4499 " (cutoff:3.500A) Processing helix chain 'H' and resid 4568 through 4594 Processing helix chain 'H' and resid 4595 through 4613 Processing helix chain 'H' and resid 4629 through 4631 No H-bonds generated for 'chain 'H' and resid 4629 through 4631' Processing helix chain 'H' and resid 4632 through 4637 removed outlier: 3.925A pdb=" N ILE H4636 " --> pdb=" O ASP H4632 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN H4637 " --> pdb=" O ARG H4633 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 4632 through 4637' Processing helix chain 'H' and resid 4642 through 4646 removed outlier: 3.873A pdb=" N TYR H4645 " --> pdb=" O PRO H4642 " (cutoff:3.500A) Processing helix chain 'H' and resid 4648 through 4663 removed outlier: 3.876A pdb=" N ARG H4652 " --> pdb=" O LYS H4648 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H4658 " --> pdb=" O VAL H4654 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY H4659 " --> pdb=" O MET H4655 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU H4660 " --> pdb=" O ASP H4656 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE H4661 " --> pdb=" O LYS H4657 " (cutoff:3.500A) Processing helix chain 'H' and resid 4663 through 4672 Processing helix chain 'H' and resid 4703 through 4715 Processing helix chain 'H' and resid 4717 through 4736 Processing helix chain 'H' and resid 4738 through 4744 removed outlier: 4.177A pdb=" N ALA H4741 " --> pdb=" O PHE H4738 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS H4743 " --> pdb=" O PHE H4740 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU H4744 " --> pdb=" O ALA H4741 " (cutoff:3.500A) Processing helix chain 'H' and resid 4745 through 4749 Processing helix chain 'H' and resid 4751 through 4763 removed outlier: 4.180A pdb=" N ARG H4755 " --> pdb=" O PHE H4751 " (cutoff:3.500A) Processing helix chain 'H' and resid 4764 through 4789 removed outlier: 3.524A pdb=" N PHE H4789 " --> pdb=" O VAL H4785 " (cutoff:3.500A) Processing helix chain 'H' and resid 4809 through 4823 removed outlier: 3.741A pdb=" N ARG H4823 " --> pdb=" O TYR H4819 " (cutoff:3.500A) Processing helix chain 'H' and resid 4838 through 4885 removed outlier: 3.740A pdb=" N TYR H4843 " --> pdb=" O GLU H4839 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H4857 " --> pdb=" O PHE H4853 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE H4858 " --> pdb=" O PHE H4854 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY H4865 " --> pdb=" O ALA H4861 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU H4866 " --> pdb=" O ILE H4862 " (cutoff:3.500A) Processing helix chain 'H' and resid 4904 through 4914 removed outlier: 3.560A pdb=" N THR H4908 " --> pdb=" O HIS H4904 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS H4914 " --> pdb=" O THR H4910 " (cutoff:3.500A) Processing helix chain 'H' and resid 4916 through 4929 removed outlier: 3.841A pdb=" N LEU H4920 " --> pdb=" O LEU H4916 " (cutoff:3.500A) Processing helix chain 'H' and resid 4935 through 4948 Processing helix chain 'H' and resid 4958 through 4963 removed outlier: 4.024A pdb=" N TYR H4963 " --> pdb=" O PHE H4959 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 5.081A pdb=" N THR A 6 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 73 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 29 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP A 100 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 8 removed outlier: 5.081A pdb=" N THR A 6 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 73 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 23 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 48 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 147 through 150 removed outlier: 3.854A pdb=" N MET B 128 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU B 121 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N CYS B 132 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 14.777A pdb=" N ILE B 119 " --> pdb=" O CYS B 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 150 removed outlier: 3.854A pdb=" N MET B 128 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU B 121 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N CYS B 132 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 14.777A pdb=" N ILE B 119 " --> pdb=" O CYS B 132 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 71 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ARG B 122 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 69 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU B 19 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 21 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 215 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 39 Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 195 Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AA9, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'B' and resid 295 through 296 removed outlier: 3.877A pdb=" N CYS B 361 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 403 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 305 through 309 Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 374 Processing sheet with id=AB4, first strand: chain 'B' and resid 645 through 647 removed outlier: 3.808A pdb=" N GLN B 645 " --> pdb=" O HIS B1631 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B1629 " --> pdb=" O ARG B 647 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 653 through 654 Processing sheet with id=AB6, first strand: chain 'B' and resid 656 through 657 Processing sheet with id=AB7, first strand: chain 'B' and resid 773 through 774 Processing sheet with id=AB8, first strand: chain 'B' and resid 722 through 723 removed outlier: 3.694A pdb=" N ALA B 698 " --> pdb=" O PHE B 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 789 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1149 through 1151 removed outlier: 3.510A pdb=" N GLN B1143 " --> pdb=" O ASP B1138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B1206 " --> pdb=" O ARG B1114 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B1252 " --> pdb=" O ILE B1087 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1180 through 1181 Processing sheet with id=AC2, first strand: chain 'B' and resid 1180 through 1181 removed outlier: 3.564A pdb=" N PHE B1103 " --> pdb=" O CYS B1164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B1104 " --> pdb=" O ASN B1216 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1442 through 1446 Processing sheet with id=AC4, first strand: chain 'B' and resid 1518 through 1522 removed outlier: 3.527A pdb=" N THR B1521 " --> pdb=" O ILE B1507 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1727 through 1728 removed outlier: 6.292A pdb=" N VAL B1727 " --> pdb=" O ILE B2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 2743 through 2744 removed outlier: 5.561A pdb=" N ILE B2743 " --> pdb=" O GLN B2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 4134 through 4139 Processing sheet with id=AC8, first strand: chain 'B' and resid 4521 through 4522 removed outlier: 3.556A pdb=" N TYR B4560 " --> pdb=" O LYS B4522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 5 through 8 removed outlier: 5.080A pdb=" N THR C 6 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS C 73 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET C 29 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP C 100 " --> pdb=" O THR C 27 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 5 through 8 removed outlier: 5.080A pdb=" N THR C 6 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYS C 73 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 23 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 48 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 147 through 150 removed outlier: 3.854A pdb=" N MET D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU D 121 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N CYS D 132 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 14.778A pdb=" N ILE D 119 " --> pdb=" O CYS D 132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 147 through 150 removed outlier: 3.854A pdb=" N MET D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU D 121 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N CYS D 132 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 14.778A pdb=" N ILE D 119 " --> pdb=" O CYS D 132 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN D 71 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ARG D 122 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU D 69 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU D 19 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 21 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA D 215 " --> pdb=" O VAL D 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 26 through 28 Processing sheet with id=AD5, first strand: chain 'D' and resid 35 through 39 Processing sheet with id=AD6, first strand: chain 'D' and resid 191 through 195 Processing sheet with id=AD7, first strand: chain 'D' and resid 233 through 234 Processing sheet with id=AD8, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AD9, first strand: chain 'D' and resid 295 through 296 removed outlier: 3.877A pdb=" N CYS D 361 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU D 403 " --> pdb=" O CYS D 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 305 through 309 Processing sheet with id=AE2, first strand: chain 'D' and resid 371 through 374 Processing sheet with id=AE3, first strand: chain 'D' and resid 645 through 647 removed outlier: 3.809A pdb=" N GLN D 645 " --> pdb=" O HIS D1631 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D1629 " --> pdb=" O ARG D 647 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 653 through 654 Processing sheet with id=AE5, first strand: chain 'D' and resid 656 through 657 Processing sheet with id=AE6, first strand: chain 'D' and resid 773 through 774 Processing sheet with id=AE7, first strand: chain 'D' and resid 722 through 723 removed outlier: 3.693A pdb=" N ALA D 698 " --> pdb=" O PHE D 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D 789 " --> pdb=" O ALA D 698 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1149 through 1151 removed outlier: 3.510A pdb=" N GLN D1143 " --> pdb=" O ASP D1138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D1206 " --> pdb=" O ARG D1114 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D1252 " --> pdb=" O ILE D1087 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1180 through 1181 Processing sheet with id=AF1, first strand: chain 'D' and resid 1180 through 1181 removed outlier: 3.564A pdb=" N PHE D1103 " --> pdb=" O CYS D1164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU D1104 " --> pdb=" O ASN D1216 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1442 through 1446 Processing sheet with id=AF3, first strand: chain 'D' and resid 1518 through 1522 removed outlier: 3.528A pdb=" N THR D1521 " --> pdb=" O ILE D1507 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1727 through 1728 removed outlier: 6.292A pdb=" N VAL D1727 " --> pdb=" O ILE D2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 2743 through 2744 removed outlier: 5.561A pdb=" N ILE D2743 " --> pdb=" O GLN D2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 4134 through 4139 Processing sheet with id=AF7, first strand: chain 'D' and resid 4521 through 4522 removed outlier: 3.555A pdb=" N TYR D4560 " --> pdb=" O LYS D4522 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 5 through 8 removed outlier: 5.081A pdb=" N THR E 6 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS E 73 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET E 29 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP E 100 " --> pdb=" O THR E 27 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 5 through 8 removed outlier: 5.081A pdb=" N THR E 6 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS E 73 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL E 23 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE E 48 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 147 through 150 removed outlier: 3.854A pdb=" N MET F 128 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU F 121 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N CYS F 132 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 14.777A pdb=" N ILE F 119 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 147 through 150 removed outlier: 3.854A pdb=" N MET F 128 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU F 121 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N CYS F 132 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 14.777A pdb=" N ILE F 119 " --> pdb=" O CYS F 132 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN F 71 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ARG F 122 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU F 69 " --> pdb=" O ARG F 122 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU F 19 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL F 21 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA F 215 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 26 through 28 Processing sheet with id=AG4, first strand: chain 'F' and resid 35 through 39 Processing sheet with id=AG5, first strand: chain 'F' and resid 191 through 195 Processing sheet with id=AG6, first strand: chain 'F' and resid 233 through 234 Processing sheet with id=AG7, first strand: chain 'F' and resid 244 through 246 Processing sheet with id=AG8, first strand: chain 'F' and resid 295 through 296 removed outlier: 3.876A pdb=" N CYS F 361 " --> pdb=" O LEU F 403 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU F 403 " --> pdb=" O CYS F 361 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 305 through 309 Processing sheet with id=AH1, first strand: chain 'F' and resid 371 through 374 Processing sheet with id=AH2, first strand: chain 'F' and resid 645 through 647 removed outlier: 3.807A pdb=" N GLN F 645 " --> pdb=" O HIS F1631 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER F1629 " --> pdb=" O ARG F 647 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 653 through 654 Processing sheet with id=AH4, first strand: chain 'F' and resid 656 through 657 Processing sheet with id=AH5, first strand: chain 'F' and resid 773 through 774 Processing sheet with id=AH6, first strand: chain 'F' and resid 722 through 723 removed outlier: 3.694A pdb=" N ALA F 698 " --> pdb=" O PHE F 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE F 789 " --> pdb=" O ALA F 698 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 1149 through 1151 removed outlier: 3.510A pdb=" N GLN F1143 " --> pdb=" O ASP F1138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F1206 " --> pdb=" O ARG F1114 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE F1087 " --> pdb=" O SER F1252 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER F1252 " --> pdb=" O ILE F1087 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 1180 through 1181 Processing sheet with id=AH9, first strand: chain 'F' and resid 1180 through 1181 removed outlier: 3.565A pdb=" N PHE F1103 " --> pdb=" O CYS F1164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU F1104 " --> pdb=" O ASN F1216 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL F1212 " --> pdb=" O VAL F1108 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 1442 through 1446 Processing sheet with id=AI2, first strand: chain 'F' and resid 1518 through 1522 removed outlier: 3.527A pdb=" N THR F1521 " --> pdb=" O ILE F1507 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 1727 through 1728 removed outlier: 6.293A pdb=" N VAL F1727 " --> pdb=" O ILE F2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'F' and resid 2743 through 2744 removed outlier: 5.561A pdb=" N ILE F2743 " --> pdb=" O GLN F2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'F' and resid 4134 through 4139 Processing sheet with id=AI6, first strand: chain 'F' and resid 4521 through 4522 removed outlier: 3.556A pdb=" N TYR F4560 " --> pdb=" O LYS F4522 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'G' and resid 5 through 8 removed outlier: 5.081A pdb=" N THR G 6 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS G 73 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET G 29 " --> pdb=" O ILE G 98 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP G 100 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'G' and resid 5 through 8 removed outlier: 5.081A pdb=" N THR G 6 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS G 73 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL G 23 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE G 48 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'H' and resid 147 through 150 removed outlier: 3.855A pdb=" N MET H 128 " --> pdb=" O HIS H 123 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU H 121 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N CYS H 132 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 14.777A pdb=" N ILE H 119 " --> pdb=" O CYS H 132 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'H' and resid 147 through 150 removed outlier: 3.855A pdb=" N MET H 128 " --> pdb=" O HIS H 123 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU H 121 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N CYS H 132 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 14.777A pdb=" N ILE H 119 " --> pdb=" O CYS H 132 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN H 71 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ARG H 122 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU H 69 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLU H 19 " --> pdb=" O ILE H 217 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL H 21 " --> pdb=" O ALA H 215 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA H 215 " --> pdb=" O VAL H 21 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'H' and resid 26 through 28 Processing sheet with id=AJ3, first strand: chain 'H' and resid 35 through 39 Processing sheet with id=AJ4, first strand: chain 'H' and resid 191 through 195 Processing sheet with id=AJ5, first strand: chain 'H' and resid 233 through 234 Processing sheet with id=AJ6, first strand: chain 'H' and resid 244 through 246 Processing sheet with id=AJ7, first strand: chain 'H' and resid 295 through 296 removed outlier: 3.877A pdb=" N CYS H 361 " --> pdb=" O LEU H 403 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU H 403 " --> pdb=" O CYS H 361 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 305 through 309 Processing sheet with id=AJ9, first strand: chain 'H' and resid 371 through 374 Processing sheet with id=AK1, first strand: chain 'H' and resid 645 through 647 removed outlier: 3.808A pdb=" N GLN H 645 " --> pdb=" O HIS H1631 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER H1629 " --> pdb=" O ARG H 647 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'H' and resid 653 through 654 Processing sheet with id=AK3, first strand: chain 'H' and resid 656 through 657 Processing sheet with id=AK4, first strand: chain 'H' and resid 773 through 774 Processing sheet with id=AK5, first strand: chain 'H' and resid 722 through 723 removed outlier: 3.694A pdb=" N ALA H 698 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE H 789 " --> pdb=" O ALA H 698 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'H' and resid 1149 through 1151 removed outlier: 3.510A pdb=" N GLN H1143 " --> pdb=" O ASP H1138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER H1206 " --> pdb=" O ARG H1114 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE H1087 " --> pdb=" O SER H1252 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER H1252 " --> pdb=" O ILE H1087 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'H' and resid 1180 through 1181 Processing sheet with id=AK8, first strand: chain 'H' and resid 1180 through 1181 removed outlier: 3.564A pdb=" N PHE H1103 " --> pdb=" O CYS H1164 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU H1104 " --> pdb=" O ASN H1216 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL H1212 " --> pdb=" O VAL H1108 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H' and resid 1442 through 1446 Processing sheet with id=AL1, first strand: chain 'H' and resid 1518 through 1522 removed outlier: 3.527A pdb=" N THR H1521 " --> pdb=" O ILE H1507 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'H' and resid 1727 through 1728 removed outlier: 6.291A pdb=" N VAL H1727 " --> pdb=" O ILE H2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'H' and resid 2743 through 2744 removed outlier: 5.561A pdb=" N ILE H2743 " --> pdb=" O GLN H2755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL3 Processing sheet with id=AL4, first strand: chain 'H' and resid 4134 through 4139 Processing sheet with id=AL5, first strand: chain 'H' and resid 4521 through 4522 removed outlier: 3.555A pdb=" N TYR H4560 " --> pdb=" O LYS H4522 " (cutoff:3.500A) 5688 hydrogen bonds defined for protein. 16392 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: 71.26 Time building geometry restraints manager: 35.31 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: 31274 1.33 - 1.45: 21561 1.45 - 1.57: 57993 1.57 - 1.70: 0 1.70 - 1.82: 1040 Bond restraints: 111868 Sorted by residual: bond pdb=" C LEU D3612 " pdb=" N PRO D3613 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.44e-02 4.82e+03 1.37e+01 bond pdb=" C LEU H3612 " pdb=" N PRO H3613 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.44e-02 4.82e+03 1.33e+01 bond pdb=" C LEU B3612 " pdb=" N PRO B3613 " ideal model delta sigma weight residual 1.326 1.379 -0.053 1.44e-02 4.82e+03 1.33e+01 bond pdb=" C LEU F3612 " pdb=" N PRO F3613 " ideal model delta sigma weight residual 1.326 1.378 -0.052 1.44e-02 4.82e+03 1.30e+01 bond pdb=" C LEU D1539 " pdb=" N PHE D1540 " ideal model delta sigma weight residual 1.327 1.267 0.060 1.71e-02 3.42e+03 1.23e+01 ... (remaining 111863 not shown) Histogram of bond angle deviations from ideal: 93.30 - 101.58: 364 101.58 - 109.86: 18998 109.86 - 118.14: 65875 118.14 - 126.41: 64399 126.41 - 134.69: 1612 Bond angle restraints: 151248 Sorted by residual: angle pdb=" N TYR D2039 " pdb=" CA TYR D2039 " pdb=" C TYR D2039 " ideal model delta sigma weight residual 113.38 123.22 -9.84 1.17e+00 7.31e-01 7.07e+01 angle pdb=" N TYR B2039 " pdb=" CA TYR B2039 " pdb=" C TYR B2039 " ideal model delta sigma weight residual 113.38 123.19 -9.81 1.17e+00 7.31e-01 7.04e+01 angle pdb=" N TYR F2039 " pdb=" CA TYR F2039 " pdb=" C TYR F2039 " ideal model delta sigma weight residual 113.38 123.18 -9.80 1.17e+00 7.31e-01 7.02e+01 angle pdb=" N TYR H2039 " pdb=" CA TYR H2039 " pdb=" C TYR H2039 " ideal model delta sigma weight residual 113.38 123.16 -9.78 1.17e+00 7.31e-01 6.99e+01 angle pdb=" C TYR D2039 " pdb=" N LEU D2040 " pdb=" CA LEU D2040 " ideal model delta sigma weight residual 121.70 134.69 -12.99 1.80e+00 3.09e-01 5.21e+01 ... (remaining 151243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 62548 16.79 - 33.58: 3378 33.58 - 50.37: 671 50.37 - 67.16: 48 67.16 - 83.95: 84 Dihedral angle restraints: 66729 sinusoidal: 25205 harmonic: 41524 Sorted by residual: dihedral pdb=" CA SER H2232 " pdb=" C SER H2232 " pdb=" N PRO H2233 " pdb=" CA PRO H2233 " ideal model delta harmonic sigma weight residual 180.00 110.73 69.27 0 5.00e+00 4.00e-02 1.92e+02 dihedral pdb=" CA SER F2232 " pdb=" C SER F2232 " pdb=" N PRO F2233 " pdb=" CA PRO F2233 " ideal model delta harmonic sigma weight residual 180.00 110.74 69.26 0 5.00e+00 4.00e-02 1.92e+02 dihedral pdb=" CA SER D2232 " pdb=" C SER D2232 " pdb=" N PRO D2233 " pdb=" CA PRO D2233 " ideal model delta harmonic sigma weight residual 180.00 110.76 69.24 0 5.00e+00 4.00e-02 1.92e+02 ... (remaining 66726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 13544 0.069 - 0.137: 3057 0.137 - 0.206: 379 0.206 - 0.274: 60 0.274 - 0.343: 16 Chirality restraints: 17056 Sorted by residual: chirality pdb=" CB THR H 854 " pdb=" CA THR H 854 " pdb=" OG1 THR H 854 " pdb=" CG2 THR H 854 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB THR B 854 " pdb=" CA THR B 854 " pdb=" OG1 THR B 854 " pdb=" CG2 THR B 854 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB THR F 854 " pdb=" CA THR F 854 " pdb=" OG1 THR F 854 " pdb=" CG2 THR F 854 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 17053 not shown) Planarity restraints: 19468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D2232 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO D2233 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO D2233 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D2233 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F2232 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO F2233 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO F2233 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO F2233 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B2232 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B2233 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO B2233 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B2233 " 0.057 5.00e-02 4.00e+02 ... (remaining 19465 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 5840 2.72 - 3.26: 113423 3.26 - 3.81: 191965 3.81 - 4.35: 224236 4.35 - 4.90: 356096 Nonbonded interactions: 891560 Sorted by model distance: nonbonded pdb=" O ILE F4891 " pdb="ZN ZN F6000 " model vdw 2.171 2.230 nonbonded pdb=" O ILE B4891 " pdb="ZN ZN B6000 " model vdw 2.171 2.230 nonbonded pdb=" O ILE H4891 " pdb="ZN ZN H6000 " model vdw 2.171 2.230 nonbonded pdb=" O ILE D4891 " pdb="ZN ZN D6000 " model vdw 2.171 2.230 nonbonded pdb=" O TYR B4568 " pdb=" OG1 THR B4572 " model vdw 2.223 2.440 ... (remaining 891555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.99 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 17.410 Check model and map are aligned: 1.240 Set scattering table: 0.810 Process input model: 264.900 Find NCS groups from input model: 5.650 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 295.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 111868 Z= 0.441 Angle : 1.132 13.497 151248 Z= 0.610 Chirality : 0.058 0.343 17056 Planarity : 0.007 0.104 19468 Dihedral : 11.535 83.953 39801 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.31 % Favored : 88.29 % Rotamer: Outliers : 0.73 % Allowed : 3.86 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.53 % Twisted Proline : 4.07 % Twisted General : 0.70 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.06), residues: 13880 helix: -1.95 (0.05), residues: 6900 sheet: -3.31 (0.13), residues: 1264 loop : -3.42 (0.07), residues: 5716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP H4950 HIS 0.019 0.003 HIS D 651 PHE 0.041 0.003 PHE H3791 TYR 0.026 0.003 TYR H2720 ARG 0.009 0.001 ARG H3860 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27760 Ramachandran restraints generated. 13880 Oldfield, 0 Emsley, 13880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27760 Ramachandran restraints generated. 13880 Oldfield, 0 Emsley, 13880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1743 time to fit residues: 5.6990 Evaluate side-chains 11 residues out of total 88 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0965 Evaluate side-chains 678 residues out of total 3065 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 656 time to evaluate : 2.293 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 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 91, in __init__ rotatable_hd = self.rotatable_hd.select(g.master_iselection)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 131, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 99, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 209, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 196, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable