Starting phenix.real_space_refine on Thu Nov 16 02:38:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdg_25828/11_2023/7tdg_25828_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdg_25828/11_2023/7tdg_25828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdg_25828/11_2023/7tdg_25828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdg_25828/11_2023/7tdg_25828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdg_25828/11_2023/7tdg_25828_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdg_25828/11_2023/7tdg_25828_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.009 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 P 16 5.49 5 S 628 5.16 5 C 74290 2.51 5 N 20743 2.21 5 O 21656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 1944": "OE1" <-> "OE2" Residue "A GLU 2115": "OE1" <-> "OE2" Residue "A GLU 2347": "OE1" <-> "OE2" Residue "A GLU 2348": "OE1" <-> "OE2" Residue "A GLU 2803": "OE1" <-> "OE2" Residue "A GLU 2915": "OE1" <-> "OE2" Residue "A GLU 3665": "OE1" <-> "OE2" Residue "A GLU 3777": "OE1" <-> "OE2" Residue "A GLU 3789": "OE1" <-> "OE2" Residue "A GLU 3811": "OE1" <-> "OE2" Residue "A GLU 3848": "OE1" <-> "OE2" Residue "A GLU 3893": "OE1" <-> "OE2" Residue "A GLU 3928": "OE1" <-> "OE2" Residue "A GLU 4015": "OE1" <-> "OE2" Residue "A PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4739": "OE1" <-> "OE2" Residue "A TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4976": "OE1" <-> "OE2" Residue "A GLU 4982": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 555": "OE1" <-> "OE2" Residue "C GLU 562": "OE1" <-> "OE2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1944": "OE1" <-> "OE2" Residue "C GLU 2347": "OE1" <-> "OE2" Residue "C GLU 2348": "OE1" <-> "OE2" Residue "C GLU 2803": "OE1" <-> "OE2" Residue "C GLU 2915": "OE1" <-> "OE2" Residue "C GLU 3665": "OE1" <-> "OE2" Residue "C GLU 3777": "OE1" <-> "OE2" Residue "C GLU 3789": "OE1" <-> "OE2" Residue "C GLU 3893": "OE1" <-> "OE2" Residue "C GLU 3928": "OE1" <-> "OE2" Residue "C GLU 4015": "OE1" <-> "OE2" Residue "C TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4976": "OE1" <-> "OE2" Residue "C GLU 4982": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1944": "OE1" <-> "OE2" Residue "D GLU 2115": "OE1" <-> "OE2" Residue "D GLU 2348": "OE1" <-> "OE2" Residue "D GLU 2803": "OE1" <-> "OE2" Residue "D GLU 2915": "OE1" <-> "OE2" Residue "D GLU 3665": "OE1" <-> "OE2" Residue "D GLU 3777": "OE1" <-> "OE2" Residue "D GLU 3789": "OE1" <-> "OE2" Residue "D GLU 3811": "OE1" <-> "OE2" Residue "D GLU 3893": "OE1" <-> "OE2" Residue "D GLU 3928": "OE1" <-> "OE2" Residue "D GLU 4015": "OE1" <-> "OE2" Residue "D TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4900": "OE1" <-> "OE2" Residue "D GLU 4982": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1797": "NH1" <-> "NH2" Residue "B GLU 1944": "OE1" <-> "OE2" Residue "B GLU 1956": "OE1" <-> "OE2" Residue "B GLU 2115": "OE1" <-> "OE2" Residue "B GLU 2347": "OE1" <-> "OE2" Residue "B GLU 2348": "OE1" <-> "OE2" Residue "B GLU 2803": "OE1" <-> "OE2" Residue "B GLU 2915": "OE1" <-> "OE2" Residue "B GLU 3665": "OE1" <-> "OE2" Residue "B GLU 3777": "OE1" <-> "OE2" Residue "B GLU 3789": "OE1" <-> "OE2" Residue "B GLU 3848": "OE1" <-> "OE2" Residue "B GLU 3893": "OE1" <-> "OE2" Residue "B GLU 3928": "OE1" <-> "OE2" Residue "B GLU 4015": "OE1" <-> "OE2" Residue "B TYR 4629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4892": "NH1" <-> "NH2" Residue "B GLU 4976": "OE1" <-> "OE2" Residue "B GLU 4982": "OE1" <-> "OE2" Time to flip residues: 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 117345 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 29247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29247 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1200} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2879 Unresolved non-hydrogen angles: 4042 Unresolved non-hydrogen dihedrals: 1770 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1661 Chain: "C" Number of atoms: 29244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29244 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1200} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2882 Unresolved non-hydrogen angles: 4045 Unresolved non-hydrogen dihedrals: 1773 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 77, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 1666 Chain: "D" Number of atoms: 29228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29228 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1204} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2898 Unresolved non-hydrogen angles: 4065 Unresolved non-hydrogen dihedrals: 1785 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 78, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 1675 Chain: "B" Number of atoms: 29246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4134, 29246 Classifications: {'peptide': 4134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1200} Link IDs: {'PTRANS': 152, 'TRANS': 3981} Chain breaks: 24 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2880 Unresolved non-hydrogen angles: 4043 Unresolved non-hydrogen dihedrals: 1771 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'UNK:plan-1': 900, 'ASP:plan': 37, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 78, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1665 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 95 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1, 'POV': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 111 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 79 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 95 Unusual residues: {' CA': 2, ' ZN': 1, 'ACP': 1, 'POV': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 10 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28572 SG CYS A4958 180.001 205.446 101.633 1.00 44.07 S ATOM 28597 SG CYS A4961 178.459 204.576 98.160 1.00 55.95 S ATOM 57816 SG CYS C4958 206.635 181.010 101.616 1.00 45.51 S ATOM 57841 SG CYS C4961 208.431 182.300 98.433 1.00 58.59 S ATOM 87044 SG CYS D4958 205.431 206.761 101.625 1.00 44.61 S ATOM 87069 SG CYS D4961 204.550 208.298 98.154 1.00 57.76 S ATOM A0CKI SG CYS B4958 181.408 180.189 101.673 1.00 46.27 S ATOM A0CL7 SG CYS B4961 182.423 178.299 98.126 1.00 61.17 S Time building chain proxies: 43.77, per 1000 atoms: 0.37 Number of scatterers: 117345 At special positions: 0 Unit cell: (387.855, 387.855, 193.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 628 16.00 P 16 15.00 O 21656 8.00 N 20743 7.00 C 74290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.04 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.04 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.04 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.04 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: 31.97 Conformation dependent library (CDL) restraints added in 13.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5101 " pdb="ZN ZN A5101 " - pdb=" NE2 HIS A4983 " pdb="ZN ZN A5101 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4958 " pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb=" ZN C5101 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C4983 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4958 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4983 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4958 " Number of angles added : 8 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31360 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 488 helices and 56 sheets defined 54.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 29.81 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.451A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.640A pdb=" N GLU A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.818A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 256' Processing helix chain 'A' and resid 308 through 313 removed outlier: 6.181A pdb=" N THR A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 313' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.679A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 423 removed outlier: 3.780A pdb=" N ASP A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.120A pdb=" N VAL A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 4.170A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 4.510A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 removed outlier: 4.292A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 3.581A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 541' Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.999A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.752A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.346A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 578' Processing helix chain 'A' and resid 579 through 594 removed outlier: 3.644A pdb=" N LEU A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 4.124A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 601 " --> pdb=" O HIS A 597 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 removed outlier: 4.156A pdb=" N GLN A 618 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 622 " --> pdb=" O GLN A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 890 removed outlier: 4.147A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLN A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 935 removed outlier: 5.325A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 removed outlier: 6.413A pdb=" N GLU A 947 " --> pdb=" O ASP A 943 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 943 through 948' Processing helix chain 'A' and resid 956 through 961 Processing helix chain 'A' and resid 978 through 999 removed outlier: 3.973A pdb=" N THR A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 985 " --> pdb=" O GLN A 981 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 986 " --> pdb=" O THR A 982 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 987 " --> pdb=" O THR A 983 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP A 999 " --> pdb=" O VAL A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 Processing helix chain 'A' and resid 1030 through 1047 removed outlier: 3.661A pdb=" N ASP A1037 " --> pdb=" O ARG A1033 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1581 removed outlier: 4.124A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET A1579 " --> pdb=" O LEU A1575 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1574 through 1581' Processing helix chain 'A' and resid 1649 through 1654 removed outlier: 4.245A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1654' Processing helix chain 'A' and resid 1656 through 1675 removed outlier: 5.924A pdb=" N GLN A1660 " --> pdb=" O ARG A1656 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG A1661 " --> pdb=" O LEU A1657 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A1674 " --> pdb=" O TYR A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 4.708A pdb=" N ALA A1682 " --> pdb=" O ASN A1678 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HIS A1683 " --> pdb=" O ASN A1679 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP A1690 " --> pdb=" O CYS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1700 removed outlier: 3.715A pdb=" N LEU A1698 " --> pdb=" O LEU A1694 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1719 removed outlier: 6.763A pdb=" N ARG A1708 " --> pdb=" O PRO A1704 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A1709 " --> pdb=" O GLY A1705 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS A1719 " --> pdb=" O LEU A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1732 removed outlier: 4.385A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 4.315A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1759 removed outlier: 4.437A pdb=" N ARG A1759 " --> pdb=" O GLY A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.758A pdb=" N LEU A1807 " --> pdb=" O PRO A1803 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A1809 " --> pdb=" O GLU A1805 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1812 " --> pdb=" O ARG A1808 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A1819 " --> pdb=" O LEU A1815 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A1820 " --> pdb=" O GLY A1816 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix removed outlier: 3.533A pdb=" N MET A1851 " --> pdb=" O THR A1847 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1855 through 1865 removed outlier: 4.352A pdb=" N MET A1865 " --> pdb=" O GLN A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1871 removed outlier: 3.628A pdb=" N PHE A1871 " --> pdb=" O GLU A1867 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1984 removed outlier: 4.062A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A1946 " --> pdb=" O LEU A1942 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A1950 " --> pdb=" O PHE A1946 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1951 " --> pdb=" O CYS A1947 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A1963 " --> pdb=" O ALA A1959 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A1964 " --> pdb=" O ALA A1960 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A1975 " --> pdb=" O ALA A1971 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 1999 removed outlier: 4.145A pdb=" N ARG A1996 " --> pdb=" O ALA A1992 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2015 removed outlier: 3.695A pdb=" N LEU A2009 " --> pdb=" O GLN A2005 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A2010 " --> pdb=" O ILE A2006 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A2011 " --> pdb=" O ASN A2007 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A2012 " --> pdb=" O MET A2008 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A2013 " --> pdb=" O LEU A2009 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A2015 " --> pdb=" O HIS A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2043 removed outlier: 4.807A pdb=" N LEU A2031 " --> pdb=" O ILE A2027 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A2032 " --> pdb=" O ARG A2028 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.698A pdb=" N VAL A2103 " --> pdb=" O SER A2099 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.738A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2142 Proline residue: A2139 - end of helix removed outlier: 5.685A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 3.714A pdb=" N THR A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A2154 " --> pdb=" O GLU A2150 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A2155 " --> pdb=" O ASP A2151 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A2161 " --> pdb=" O GLU A2157 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A2166 " --> pdb=" O ILE A2162 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2188 removed outlier: 3.695A pdb=" N ASN A2176 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A2186 " --> pdb=" O ILE A2182 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A2187 " --> pdb=" O GLY A2183 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2195 removed outlier: 4.478A pdb=" N GLN A2193 " --> pdb=" O LYS A2189 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS A2194 " --> pdb=" O VAL A2190 " (cutoff:3.500A) Proline residue: A2195 - end of helix No H-bonds generated for 'chain 'A' and resid 2189 through 2195' Processing helix chain 'A' and resid 2196 through 2202 Processing helix chain 'A' and resid 2203 through 2216 removed outlier: 3.799A pdb=" N ASN A2213 " --> pdb=" O GLU A2209 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A2215 " --> pdb=" O MET A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2225 through 2244 removed outlier: 4.722A pdb=" N VAL A2229 " --> pdb=" O PHE A2225 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A2230 " --> pdb=" O PRO A2226 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER A2231 " --> pdb=" O LYS A2227 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2255 removed outlier: 3.751A pdb=" N SER A2249 " --> pdb=" O GLN A2245 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A2252 " --> pdb=" O ARG A2248 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER A2255 " --> pdb=" O PHE A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2265 removed outlier: 3.615A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A2264 " --> pdb=" O ASN A2260 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2282 removed outlier: 3.748A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A2276 " --> pdb=" O PRO A2272 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A2282 " --> pdb=" O ALA A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2291 removed outlier: 3.595A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN A2291 " --> pdb=" O ALA A2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2286 through 2291' Processing helix chain 'A' and resid 2294 through 2309 removed outlier: 3.619A pdb=" N VAL A2299 " --> pdb=" O LEU A2295 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A2300 " --> pdb=" O GLU A2296 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A2301 " --> pdb=" O LYS A2297 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A2302 " --> pdb=" O VAL A2298 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A2307 " --> pdb=" O ALA A2303 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2315 removed outlier: 3.685A pdb=" N LEU A2314 " --> pdb=" O CYS A2310 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2340 removed outlier: 3.567A pdb=" N ARG A2330 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A2331 " --> pdb=" O GLY A2327 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A2332 " --> pdb=" O GLY A2328 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP A2333 " --> pdb=" O GLU A2329 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A2335 " --> pdb=" O TYR A2331 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A2337 " --> pdb=" O ASP A2333 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.891A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A2359 " --> pdb=" O ARG A2355 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2365 through 2370 Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2438 Proline residue: A2438 - end of helix Processing helix chain 'A' and resid 2440 through 2447 removed outlier: 3.634A pdb=" N GLY A2446 " --> pdb=" O LEU A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2448 through 2462 removed outlier: 4.148A pdb=" N ARG A2452 " --> pdb=" O GLY A2448 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A2453 " --> pdb=" O GLU A2449 " (cutoff:3.500A) Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2464 through 2472 removed outlier: 3.931A pdb=" N GLY A2468 " --> pdb=" O ASP A2464 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A2469 " --> pdb=" O ASP A2465 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A2471 " --> pdb=" O VAL A2467 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A2472 " --> pdb=" O GLY A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2751 through 2774 removed outlier: 4.422A pdb=" N ILE A2755 " --> pdb=" O LEU A2751 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A2758 " --> pdb=" O PHE A2754 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A2759 " --> pdb=" O ILE A2755 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A2762 " --> pdb=" O PHE A2758 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS A2763 " --> pdb=" O ALA A2759 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU A2764 " --> pdb=" O GLU A2760 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS A2765 " --> pdb=" O TYR A2761 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP A2766 " --> pdb=" O THR A2762 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A2767 " --> pdb=" O HIS A2763 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE A2768 " --> pdb=" O GLU A2764 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP A2769 " --> pdb=" O LYS A2765 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYS A2770 " --> pdb=" O TRP A2766 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE A2771 " --> pdb=" O ALA A2767 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A2772 " --> pdb=" O PHE A2768 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A2773 " --> pdb=" O ASP A2769 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2804 removed outlier: 4.903A pdb=" N LYS A2802 " --> pdb=" O SER A2798 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2896 removed outlier: 5.419A pdb=" N GLU A2876 " --> pdb=" O GLN A2872 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN A2877 " --> pdb=" O ALA A2873 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A2879 " --> pdb=" O ALA A2875 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN A2881 " --> pdb=" O GLN A2877 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR A2882 " --> pdb=" O LEU A2878 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A2883 " --> pdb=" O ALA A2879 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A2890 " --> pdb=" O TRP A2886 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS A2891 " --> pdb=" O GLY A2887 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN A2892 " --> pdb=" O ARG A2888 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU A2894 " --> pdb=" O LYS A2890 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA A2896 " --> pdb=" O GLN A2892 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2930 removed outlier: 4.243A pdb=" N ALA A2923 " --> pdb=" O ASP A2919 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A2925 " --> pdb=" O GLU A2921 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS A2928 " --> pdb=" O GLN A2924 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A2929 " --> pdb=" O GLU A2925 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A2930 " --> pdb=" O LEU A2926 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3657 removed outlier: 3.669A pdb=" N LEU A3654 " --> pdb=" O CYS A3650 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU A3655 " --> pdb=" O ASN A3651 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A3656 " --> pdb=" O MET A3652 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TYR A3657 " --> pdb=" O PHE A3653 " (cutoff:3.500A) Processing helix chain 'A' and resid 3668 through 3683 removed outlier: 5.370A pdb=" N ALA A3680 " --> pdb=" O ASP A3676 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY A3681 " --> pdb=" O LEU A3677 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A3682 " --> pdb=" O SER A3678 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3712 removed outlier: 5.685A pdb=" N GLU A3712 " --> pdb=" O THR A3708 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3736 removed outlier: 3.523A pdb=" N MET A3723 " --> pdb=" O ASP A3719 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A3727 " --> pdb=" O MET A3723 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A3732 " --> pdb=" O ILE A3728 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU A3736 " --> pdb=" O SER A3732 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3761 Processing helix chain 'A' and resid 3764 through 3771 removed outlier: 4.824A pdb=" N SER A3768 " --> pdb=" O LEU A3764 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS A3771 " --> pdb=" O GLN A3767 " (cutoff:3.500A) Processing helix chain 'A' and resid 3772 through 3787 removed outlier: 3.622A pdb=" N ALA A3776 " --> pdb=" O THR A3772 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU A3777 " --> pdb=" O ARG A3773 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A3778 " --> pdb=" O GLY A3774 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS A3786 " --> pdb=" O MET A3782 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 3.946A pdb=" N LEU A3805 " --> pdb=" O GLY A3801 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 removed outlier: 3.592A pdb=" N TYR A3819 " --> pdb=" O LYS A3815 " (cutoff:3.500A) Processing helix chain 'A' and resid 3826 through 3839 removed outlier: 7.081A pdb=" N GLN A3830 " --> pdb=" O VAL A3826 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A3838 " --> pdb=" O ALA A3834 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS A3839 " --> pdb=" O LEU A3835 " (cutoff:3.500A) Processing helix chain 'A' and resid 3843 through 3858 removed outlier: 3.661A pdb=" N GLY A3855 " --> pdb=" O ASN A3851 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY A3857 " --> pdb=" O ALA A3853 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N MET A3858 " --> pdb=" O GLU A3854 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3893 removed outlier: 3.844A pdb=" N ASP A3883 " --> pdb=" O GLU A3879 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A3893 " --> pdb=" O GLN A3889 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 6.436A pdb=" N GLN A3900 " --> pdb=" O ASN A3896 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN A3901 " --> pdb=" O ASN A3897 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A3904 " --> pdb=" O GLN A3900 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A3905 " --> pdb=" O ASN A3901 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.598A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A3935 " --> pdb=" O SER A3931 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A3936 " --> pdb=" O ASP A3932 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A3937 " --> pdb=" O PHE A3933 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.695A pdb=" N LYS A3953 " --> pdb=" O ARG A3949 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA A3954 " --> pdb=" O ASN A3950 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET A3955 " --> pdb=" O PHE A3951 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A3956 " --> pdb=" O SER A3952 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A3957 " --> pdb=" O LYS A3953 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A3967 " --> pdb=" O ASN A3963 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A3968 " --> pdb=" O SER A3964 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 5.110A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4006 removed outlier: 3.518A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.578A pdb=" N LEU A4013 " --> pdb=" O GLN A4009 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A4030 " --> pdb=" O MET A4026 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU A4032 " --> pdb=" O LEU A4028 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4052 removed outlier: 6.328A pdb=" N ARG A4042 " --> pdb=" O GLY A4038 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A4043 " --> pdb=" O MET A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4053 through 4072 removed outlier: 3.852A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A4062 " --> pdb=" O ILE A4058 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A4065 " --> pdb=" O PHE A4061 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A4069 " --> pdb=" O PHE A4065 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A4071 " --> pdb=" O LYS A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4081 removed outlier: 5.022A pdb=" N TYR A4080 " --> pdb=" O ALA A4076 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A4081 " --> pdb=" O PHE A4077 " (cutoff:3.500A) Processing helix chain 'A' and resid 4090 through 4101 removed outlier: 3.734A pdb=" N GLN A4094 " --> pdb=" O LYS A4090 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A4095 " --> pdb=" O LYS A4091 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A4100 " --> pdb=" O ALA A4096 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 3.790A pdb=" N ILE A4108 " --> pdb=" O THR A4104 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN A4109 " --> pdb=" O GLY A4105 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4137 removed outlier: 5.353A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Proline residue: A4135 - end of helix Processing helix chain 'A' and resid 4138 through 4154 Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 4.224A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A4164 " --> pdb=" O LEU A4160 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A4165 " --> pdb=" O ARG A4161 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A4166 " --> pdb=" O ASN A4162 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4198 through 4207 removed outlier: 4.116A pdb=" N ARG A4202 " --> pdb=" O SER A4198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A4204 " --> pdb=" O THR A4200 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4224 removed outlier: 3.554A pdb=" N ASN A4223 " --> pdb=" O PHE A4219 " (cutoff:3.500A) Processing helix chain 'A' and resid 4229 through 4252 removed outlier: 4.163A pdb=" N SER A4252 " --> pdb=" O ALA A4248 " (cutoff:3.500A) Processing helix chain 'A' and resid 4543 through 4559 removed outlier: 4.603A pdb=" N GLN A4547 " --> pdb=" O GLU A4543 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A4557 " --> pdb=" O ASN A4553 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A4559 " --> pdb=" O LEU A4555 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4579 removed outlier: 4.202A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4643 through 4684 removed outlier: 3.576A pdb=" N THR A4651 " --> pdb=" O SER A4647 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A4658 " --> pdb=" O ALA A4654 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A4659 " --> pdb=" O PHE A4655 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A4663 " --> pdb=" O ILE A4659 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A4664 " --> pdb=" O GLY A4660 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix removed outlier: 3.595A pdb=" N ASP A4684 " --> pdb=" O LYS A4680 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4707 removed outlier: 3.569A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4729 removed outlier: 3.502A pdb=" N LEU A4725 " --> pdb=" O LYS A4721 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 removed outlier: 4.424A pdb=" N GLY A4742 " --> pdb=" O ALA A4738 " (cutoff:3.500A) Processing helix chain 'A' and resid 4749 through 4754 Processing helix chain 'A' and resid 4766 through 4771 removed outlier: 4.261A pdb=" N SER A4770 " --> pdb=" O THR A4766 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A4771 " --> pdb=" O TRP A4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4766 through 4771' Processing helix chain 'A' and resid 4772 through 4786 removed outlier: 3.984A pdb=" N ASP A4786 " --> pdb=" O VAL A4782 " (cutoff:3.500A) Processing helix chain 'A' and resid 4787 through 4803 removed outlier: 4.276A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) Processing helix chain 'A' and resid 4807 through 4820 removed outlier: 4.669A pdb=" N ALA A4811 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY A4819 " --> pdb=" O ASP A4815 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL A4820 " --> pdb=" O ILE A4816 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.816A pdb=" N THR A4825 " --> pdb=" O LYS A4821 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A4826 " --> pdb=" O THR A4822 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4858 Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 3.506A pdb=" N MET A4887 " --> pdb=" O TYR A4883 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4897 through 4902 removed outlier: 4.044A pdb=" N ILE A4901 " --> pdb=" O ILE A4897 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4897 through 4902' Processing helix chain 'A' and resid 4909 through 4924 removed outlier: 6.251A pdb=" N VAL A4914 " --> pdb=" O GLU A4910 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A4915 " --> pdb=" O LEU A4911 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4957 removed outlier: 3.652A pdb=" N ILE A4936 " --> pdb=" O ILE A4932 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A4940 " --> pdb=" O ILE A4936 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A4941 " --> pdb=" O ILE A4937 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A4950 " --> pdb=" O GLN A4946 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A4951 " --> pdb=" O GLN A4947 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A4955 " --> pdb=" O LYS A4951 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 3.850A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 removed outlier: 6.238A pdb=" N TYR A4988 " --> pdb=" O ASN A4984 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 removed outlier: 3.663A pdb=" N GLU A5016 " --> pdb=" O LYS A5012 " (cutoff:3.500A) Processing helix chain 'A' and resid 5027 through 5033 removed outlier: 6.432A pdb=" N GLN A5031 " --> pdb=" O CYS A5027 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A5032 " --> pdb=" O PHE A5028 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A5033 " --> pdb=" O ARG A5029 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5027 through 5033' Processing helix chain 'A' and resid 3865 through 3870 removed outlier: 5.590A pdb=" N ARG A3868 " --> pdb=" O VAL A3865 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN A3870 " --> pdb=" O ASN A3867 " (cutoff:3.500A) Processing helix chain 'A' and resid 4685 through 4690 removed outlier: 3.780A pdb=" N GLU A4690 " --> pdb=" O GLY A4685 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4685 through 4690' Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.440A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.622A pdb=" N GLU C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 removed outlier: 4.822A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 251 through 256' Processing helix chain 'C' and resid 308 through 313 removed outlier: 6.181A pdb=" N THR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 313' Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.685A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 423 removed outlier: 3.781A pdb=" N ASP C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 removed outlier: 4.096A pdb=" N VAL C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 442 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 452 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 482 removed outlier: 4.169A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 4.510A pdb=" N VAL C 487 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 removed outlier: 4.285A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 541 removed outlier: 3.617A pdb=" N CYS C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 539 " --> pdb=" O ALA C 535 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 541' Processing helix chain 'C' and resid 543 through 551 removed outlier: 3.973A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 3.694A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 567 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 4.352A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 572 through 578' Processing helix chain 'C' and resid 579 through 594 removed outlier: 3.644A pdb=" N LEU C 590 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP C 591 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 4.132A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 601 " --> pdb=" O HIS C 597 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 removed outlier: 4.159A pdb=" N GLN C 618 " --> pdb=" O VAL C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 890 removed outlier: 4.149A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 883 " --> pdb=" O HIS C 879 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU C 888 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLN C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 935 removed outlier: 5.328A pdb=" N LEU C 935 " --> pdb=" O THR C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 removed outlier: 6.414A pdb=" N GLU C 947 " --> pdb=" O ASP C 943 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 948 " --> pdb=" O GLU C 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 943 through 948' Processing helix chain 'C' and resid 956 through 961 Processing helix chain 'C' and resid 978 through 999 removed outlier: 3.972A pdb=" N THR C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 985 " --> pdb=" O GLN C 981 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 986 " --> pdb=" O THR C 982 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 987 " --> pdb=" O THR C 983 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP C 999 " --> pdb=" O VAL C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1005 Processing helix chain 'C' and resid 1030 through 1047 removed outlier: 3.662A pdb=" N ASP C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR C1045 " --> pdb=" O GLN C1041 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU C1046 " --> pdb=" O ALA C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1574 through 1581 removed outlier: 4.124A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET C1579 " --> pdb=" O LEU C1575 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C1581 " --> pdb=" O ALA C1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1574 through 1581' Processing helix chain 'C' and resid 1649 through 1654 removed outlier: 4.230A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1649 through 1654' Processing helix chain 'C' and resid 1656 through 1675 removed outlier: 5.925A pdb=" N GLN C1660 " --> pdb=" O ARG C1656 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG C1661 " --> pdb=" O LEU C1657 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS C1674 " --> pdb=" O TYR C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1690 removed outlier: 4.712A pdb=" N ALA C1682 " --> pdb=" O ASN C1678 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS C1683 " --> pdb=" O ASN C1679 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP C1690 " --> pdb=" O CYS C1686 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1700 removed outlier: 3.693A pdb=" N LEU C1698 " --> pdb=" O LEU C1694 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C1700 " --> pdb=" O HIS C1696 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1719 removed outlier: 6.753A pdb=" N ARG C1708 " --> pdb=" O PRO C1704 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C1709 " --> pdb=" O GLY C1705 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS C1719 " --> pdb=" O LEU C1715 " (cutoff:3.500A) Processing helix chain 'C' and resid 1720 through 1732 removed outlier: 4.381A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 4.315A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1754 through 1759 removed outlier: 4.437A pdb=" N ARG C1759 " --> pdb=" O GLY C1755 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.739A pdb=" N LEU C1807 " --> pdb=" O PRO C1803 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C1809 " --> pdb=" O GLU C1805 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C1812 " --> pdb=" O ARG C1808 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C1819 " --> pdb=" O LEU C1815 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C1820 " --> pdb=" O GLY C1816 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN C1824 " --> pdb=" O ARG C1820 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix removed outlier: 3.530A pdb=" N MET C1851 " --> pdb=" O THR C1847 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C1852 " --> pdb=" O LEU C1848 " (cutoff:3.500A) Processing helix chain 'C' and resid 1855 through 1865 removed outlier: 4.344A pdb=" N MET C1865 " --> pdb=" O GLN C1861 " (cutoff:3.500A) Processing helix chain 'C' and resid 1866 through 1871 removed outlier: 3.633A pdb=" N PHE C1871 " --> pdb=" O GLU C1867 " (cutoff:3.500A) Processing helix chain 'C' and resid 1934 through 1984 removed outlier: 4.095A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR C1945 " --> pdb=" O ASN C1941 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C1946 " --> pdb=" O LEU C1942 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C1950 " --> pdb=" O PHE C1946 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C1951 " --> pdb=" O CYS C1947 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU C1963 " --> pdb=" O ALA C1959 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG C1964 " --> pdb=" O ALA C1960 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C1975 " --> pdb=" O ALA C1971 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 1999 removed outlier: 4.142A pdb=" N ARG C1996 " --> pdb=" O ALA C1992 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2015 removed outlier: 3.695A pdb=" N LEU C2009 " --> pdb=" O GLN C2005 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C2010 " --> pdb=" O ILE C2006 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C2011 " --> pdb=" O ASN C2007 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C2012 " --> pdb=" O MET C2008 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C2013 " --> pdb=" O LEU C2009 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C2015 " --> pdb=" O HIS C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2027 through 2043 removed outlier: 4.807A pdb=" N LEU C2031 " --> pdb=" O ILE C2027 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C2032 " --> pdb=" O ARG C2028 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY C2043 " --> pdb=" O LEU C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.698A pdb=" N VAL C2103 " --> pdb=" O SER C2099 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.742A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C2126 " --> pdb=" O SER C2122 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2142 Proline residue: C2139 - end of helix removed outlier: 5.685A pdb=" N TYR C2142 " --> pdb=" O LEU C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2169 removed outlier: 3.716A pdb=" N THR C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C2154 " --> pdb=" O GLU C2150 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C2155 " --> pdb=" O ASP C2151 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C2161 " --> pdb=" O GLU C2157 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C2166 " --> pdb=" O ILE C2162 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2188 removed outlier: 3.697A pdb=" N ASN C2176 " --> pdb=" O PRO C2172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C2177 " --> pdb=" O GLN C2173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C2186 " --> pdb=" O ILE C2182 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN C2187 " --> pdb=" O GLY C2183 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN C2188 " --> pdb=" O ASN C2184 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2195 removed outlier: 4.477A pdb=" N GLN C2193 " --> pdb=" O LYS C2189 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS C2194 " --> pdb=" O VAL C2190 " (cutoff:3.500A) Proline residue: C2195 - end of helix No H-bonds generated for 'chain 'C' and resid 2189 through 2195' Processing helix chain 'C' and resid 2196 through 2202 Processing helix chain 'C' and resid 2203 through 2216 removed outlier: 3.800A pdb=" N ASN C2213 " --> pdb=" O GLU C2209 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL C2214 " --> pdb=" O VAL C2210 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C2215 " --> pdb=" O MET C2211 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2244 removed outlier: 4.722A pdb=" N VAL C2229 " --> pdb=" O PHE C2225 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR C2230 " --> pdb=" O PRO C2226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C2231 " --> pdb=" O LYS C2227 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2255 removed outlier: 3.750A pdb=" N SER C2249 " --> pdb=" O GLN C2245 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C2252 " --> pdb=" O ARG C2248 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N SER C2255 " --> pdb=" O PHE C2251 " (cutoff:3.500A) Processing helix chain 'C' and resid 2256 through 2265 removed outlier: 3.615A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C2264 " --> pdb=" O ASN C2260 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C2265 " --> pdb=" O SER C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2282 removed outlier: 3.747A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA C2276 " --> pdb=" O PRO C2272 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C2281 " --> pdb=" O ALA C2277 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP C2282 " --> pdb=" O ALA C2278 " (cutoff:3.500A) Processing helix chain 'C' and resid 2286 through 2291 removed outlier: 3.597A pdb=" N LEU C2290 " --> pdb=" O LEU C2286 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLN C2291 " --> pdb=" O ALA C2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2286 through 2291' Processing helix chain 'C' and resid 2294 through 2309 removed outlier: 3.632A pdb=" N VAL C2299 " --> pdb=" O LEU C2295 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER C2300 " --> pdb=" O GLU C2296 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C2301 " --> pdb=" O LYS C2297 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C2302 " --> pdb=" O VAL C2298 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C2307 " --> pdb=" O ALA C2303 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER C2309 " --> pdb=" O CYS C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2315 removed outlier: 3.684A pdb=" N LEU C2314 " --> pdb=" O CYS C2310 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2340 removed outlier: 3.564A pdb=" N ARG C2330 " --> pdb=" O CYS C2326 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C2331 " --> pdb=" O GLY C2327 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU C2332 " --> pdb=" O GLY C2328 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP C2333 " --> pdb=" O GLU C2329 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C2335 " --> pdb=" O TYR C2331 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C2337 " --> pdb=" O ASP C2333 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.852A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG C2359 " --> pdb=" O ARG C2355 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Proline residue: C2361 - end of helix Processing helix chain 'C' and resid 2365 through 2370 Processing helix chain 'C' and resid 2375 through 2390 Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2438 Proline residue: C2438 - end of helix Processing helix chain 'C' and resid 2440 through 2447 removed outlier: 3.634A pdb=" N GLY C2446 " --> pdb=" O LEU C2442 " (cutoff:3.500A) Processing helix chain 'C' and resid 2448 through 2462 removed outlier: 4.152A pdb=" N ARG C2452 " --> pdb=" O GLY C2448 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C2453 " --> pdb=" O GLU C2449 " (cutoff:3.500A) Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2464 through 2472 removed outlier: 3.933A pdb=" N GLY C2468 " --> pdb=" O ASP C2464 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C2469 " --> pdb=" O ASP C2465 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C2471 " --> pdb=" O VAL C2467 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C2472 " --> pdb=" O GLY C2468 " (cutoff:3.500A) Processing helix chain 'C' and resid 2751 through 2774 removed outlier: 4.419A pdb=" N ILE C2755 " --> pdb=" O LEU C2751 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C2758 " --> pdb=" O PHE C2754 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA C2759 " --> pdb=" O ILE C2755 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C2762 " --> pdb=" O PHE C2758 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N HIS C2763 " --> pdb=" O ALA C2759 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU C2764 " --> pdb=" O GLU C2760 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS C2765 " --> pdb=" O TYR C2761 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TRP C2766 " --> pdb=" O THR C2762 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C2767 " --> pdb=" O HIS C2763 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C2768 " --> pdb=" O GLU C2764 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP C2769 " --> pdb=" O LYS C2765 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS C2770 " --> pdb=" O TRP C2766 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE C2771 " --> pdb=" O ALA C2767 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN C2772 " --> pdb=" O PHE C2768 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN C2773 " --> pdb=" O ASP C2769 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2804 removed outlier: 4.904A pdb=" N LYS C2802 " --> pdb=" O SER C2798 " (cutoff:3.500A) Processing helix chain 'C' and resid 2872 through 2896 removed outlier: 5.289A pdb=" N GLU C2876 " --> pdb=" O GLN C2872 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN C2877 " --> pdb=" O ALA C2873 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C2879 " --> pdb=" O ALA C2875 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN C2881 " --> pdb=" O GLN C2877 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR C2882 " --> pdb=" O LEU C2878 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS C2890 " --> pdb=" O TRP C2886 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS C2891 " --> pdb=" O GLY C2887 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN C2892 " --> pdb=" O ARG C2888 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLU C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU C2894 " --> pdb=" O LYS C2890 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA C2896 " --> pdb=" O GLN C2892 " (cutoff:3.500A) Processing helix chain 'C' and resid 2919 through 2930 removed outlier: 4.242A pdb=" N ALA C2923 " --> pdb=" O ASP C2919 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C2925 " --> pdb=" O GLU C2921 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS C2928 " --> pdb=" O GLN C2924 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE C2929 " --> pdb=" O GLU C2925 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C2930 " --> pdb=" O LEU C2926 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3657 removed outlier: 3.669A pdb=" N LEU C3654 " --> pdb=" O CYS C3650 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER C3656 " --> pdb=" O MET C3652 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR C3657 " --> pdb=" O PHE C3653 " (cutoff:3.500A) Processing helix chain 'C' and resid 3668 through 3683 removed outlier: 5.371A pdb=" N ALA C3680 " --> pdb=" O ASP C3676 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY C3681 " --> pdb=" O LEU C3677 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU C3682 " --> pdb=" O SER C3678 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3712 removed outlier: 5.657A pdb=" N GLU C3712 " --> pdb=" O THR C3708 " (cutoff:3.500A) Processing helix chain 'C' and resid 3719 through 3736 removed outlier: 3.529A pdb=" N MET C3723 " --> pdb=" O ASP C3719 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP C3727 " --> pdb=" O MET C3723 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C3732 " --> pdb=" O ILE C3728 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU C3736 " --> pdb=" O SER C3732 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3761 Processing helix chain 'C' and resid 3764 through 3771 removed outlier: 4.824A pdb=" N SER C3768 " --> pdb=" O LEU C3764 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N HIS C3771 " --> pdb=" O GLN C3767 " (cutoff:3.500A) Processing helix chain 'C' and resid 3772 through 3787 removed outlier: 3.629A pdb=" N ALA C3776 " --> pdb=" O THR C3772 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU C3777 " --> pdb=" O ARG C3773 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C3778 " --> pdb=" O GLY C3774 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS C3786 " --> pdb=" O MET C3782 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.950A pdb=" N LEU C3805 " --> pdb=" O GLY C3801 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 removed outlier: 3.592A pdb=" N TYR C3819 " --> pdb=" O LYS C3815 " (cutoff:3.500A) Processing helix chain 'C' and resid 3826 through 3839 removed outlier: 7.089A pdb=" N GLN C3830 " --> pdb=" O VAL C3826 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C3838 " --> pdb=" O ALA C3834 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS C3839 " --> pdb=" O LEU C3835 " (cutoff:3.500A) Processing helix chain 'C' and resid 3843 through 3858 removed outlier: 3.663A pdb=" N GLY C3855 " --> pdb=" O ASN C3851 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU C3856 " --> pdb=" O LYS C3852 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY C3857 " --> pdb=" O ALA C3853 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N MET C3858 " --> pdb=" O GLU C3854 " (cutoff:3.500A) Processing helix chain 'C' and resid 3877 through 3893 removed outlier: 3.848A pdb=" N ASP C3883 " --> pdb=" O GLU C3879 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C3893 " --> pdb=" O GLN C3889 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 6.439A pdb=" N GLN C3900 " --> pdb=" O ASN C3896 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN C3901 " --> pdb=" O ASN C3897 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C3904 " --> pdb=" O GLN C3900 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C3905 " --> pdb=" O ASN C3901 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.596A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C3935 " --> pdb=" O SER C3931 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C3936 " --> pdb=" O ASP C3932 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR C3937 " --> pdb=" O PHE C3933 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.697A pdb=" N LYS C3953 " --> pdb=" O ARG C3949 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA C3954 " --> pdb=" O ASN C3950 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET C3955 " --> pdb=" O PHE C3951 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER C3956 " --> pdb=" O SER C3952 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C3957 " --> pdb=" O LYS C3953 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C3967 " --> pdb=" O ASN C3963 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR C3968 " --> pdb=" O SER C3964 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3984 removed outlier: 5.107A pdb=" N ARG C3984 " --> pdb=" O LEU C3980 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4006 removed outlier: 3.530A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.578A pdb=" N LEU C4013 " --> pdb=" O GLN C4009 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C4030 " --> pdb=" O MET C4026 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU C4032 " --> pdb=" O LEU C4028 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4052 removed outlier: 6.327A pdb=" N ARG C4042 " --> pdb=" O GLY C4038 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN C4043 " --> pdb=" O MET C4039 " (cutoff:3.500A) Processing helix chain 'C' and resid 4053 through 4072 removed outlier: 3.834A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C4062 " --> pdb=" O ILE C4058 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C4065 " --> pdb=" O PHE C4061 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C4069 " --> pdb=" O PHE C4065 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C4071 " --> pdb=" O LYS C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4081 removed outlier: 5.025A pdb=" N TYR C4080 " --> pdb=" O ALA C4076 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C4081 " --> pdb=" O PHE C4077 " (cutoff:3.500A) Processing helix chain 'C' and resid 4090 through 4101 removed outlier: 3.722A pdb=" N GLN C4094 " --> pdb=" O LYS C4090 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS C4095 " --> pdb=" O LYS C4091 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C4100 " --> pdb=" O ALA C4096 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 3.833A pdb=" N ILE C4108 " --> pdb=" O THR C4104 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN C4109 " --> pdb=" O GLY C4105 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4137 removed outlier: 5.336A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Proline residue: C4135 - end of helix Processing helix chain 'C' and resid 4138 through 4154 Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 4.226A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C4164 " --> pdb=" O LEU C4160 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU C4165 " --> pdb=" O ARG C4161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C4166 " --> pdb=" O ASN C4162 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4175 Processing helix chain 'C' and resid 4198 through 4207 removed outlier: 4.034A pdb=" N ARG C4202 " --> pdb=" O SER C4198 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C4204 " --> pdb=" O THR C4200 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N MET C4207 " --> pdb=" O ALA C4203 " (cutoff:3.500A) Processing helix chain 'C' and resid 4208 through 4224 removed outlier: 3.543A pdb=" N ASN C4223 " --> pdb=" O PHE C4219 " (cutoff:3.500A) Processing helix chain 'C' and resid 4229 through 4252 removed outlier: 4.170A pdb=" N SER C4252 " --> pdb=" O ALA C4248 " (cutoff:3.500A) Processing helix chain 'C' and resid 4543 through 4559 removed outlier: 4.610A pdb=" N GLN C4547 " --> pdb=" O GLU C4543 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C4557 " --> pdb=" O ASN C4553 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C4558 " --> pdb=" O TYR C4554 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C4559 " --> pdb=" O LEU C4555 " (cutoff:3.500A) Processing helix chain 'C' and resid 4560 through 4579 removed outlier: 4.231A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4643 through 4684 removed outlier: 3.578A pdb=" N THR C4651 " --> pdb=" O SER C4647 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C4658 " --> pdb=" O ALA C4654 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C4659 " --> pdb=" O PHE C4655 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS C4663 " --> pdb=" O ILE C4659 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C4664 " --> pdb=" O GLY C4660 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix removed outlier: 3.599A pdb=" N ASP C4684 " --> pdb=" O LYS C4680 " (cutoff:3.500A) Processing helix chain 'C' and resid 4696 through 4707 removed outlier: 3.585A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4729 removed outlier: 3.502A pdb=" N LEU C4725 " --> pdb=" O LYS C4721 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 removed outlier: 4.424A pdb=" N GLY C4742 " --> pdb=" O ALA C4738 " (cutoff:3.500A) Processing helix chain 'C' and resid 4749 through 4754 Processing helix chain 'C' and resid 4766 through 4771 removed outlier: 4.263A pdb=" N SER C4770 " --> pdb=" O THR C4766 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C4771 " --> pdb=" O TRP C4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4766 through 4771' Processing helix chain 'C' and resid 4772 through 4786 removed outlier: 3.990A pdb=" N ASP C4786 " --> pdb=" O VAL C4782 " (cutoff:3.500A) Processing helix chain 'C' and resid 4787 through 4803 removed outlier: 4.461A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) Processing helix chain 'C' and resid 4807 through 4820 removed outlier: 4.622A pdb=" N ALA C4811 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP C4815 " --> pdb=" O ALA C4811 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLY C4819 " --> pdb=" O ASP C4815 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL C4820 " --> pdb=" O ILE C4816 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.815A pdb=" N THR C4825 " --> pdb=" O LYS C4821 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C4826 " --> pdb=" O THR C4822 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4858 removed outlier: 3.510A pdb=" N PHE C4858 " --> pdb=" O VAL C4854 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.308A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4897 through 4902 removed outlier: 3.825A pdb=" N ILE C4901 " --> pdb=" O ILE C4897 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLU C4902 " --> pdb=" O GLY C4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4897 through 4902' Processing helix chain 'C' and resid 4909 through 4924 removed outlier: 6.122A pdb=" N VAL C4914 " --> pdb=" O GLU C4910 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL C4915 " --> pdb=" O LEU C4911 " (cutoff:3.500A) Processing helix chain 'C' and resid 4928 through 4957 removed outlier: 3.637A pdb=" N ILE C4936 " --> pdb=" O ILE C4932 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C4940 " --> pdb=" O ILE C4936 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY C4941 " --> pdb=" O ILE C4937 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C4950 " --> pdb=" O GLN C4946 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C4951 " --> pdb=" O GLN C4947 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C4955 " --> pdb=" O LYS C4951 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4970 removed outlier: 3.836A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 removed outlier: 6.509A pdb=" N TYR C4988 " --> pdb=" O ASN C4984 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) Processing helix chain 'C' and resid 5004 through 5017 removed outlier: 3.673A pdb=" N GLU C5016 " --> pdb=" O LYS C5012 " (cutoff:3.500A) Processing helix chain 'C' and resid 5027 through 5033 removed outlier: 6.431A pdb=" N GLN C5031 " --> pdb=" O CYS C5027 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR C5032 " --> pdb=" O PHE C5028 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C5033 " --> pdb=" O ARG C5029 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5027 through 5033' Processing helix chain 'C' and resid 3865 through 3870 removed outlier: 5.589A pdb=" N ARG C3868 " --> pdb=" O VAL C3865 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN C3870 " --> pdb=" O ASN C3867 " (cutoff:3.500A) Processing helix chain 'C' and resid 4685 through 4690 removed outlier: 3.774A pdb=" N GLU C4690 " --> pdb=" O GLY C4685 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4685 through 4690' Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.451A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 removed outlier: 3.631A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 removed outlier: 4.840A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 256' Processing helix chain 'D' and resid 308 through 313 removed outlier: 6.181A pdb=" N THR D 312 " --> pdb=" O HIS D 308 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 313' Processing helix chain 'D' and resid 364 through 371 removed outlier: 3.680A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 423 removed outlier: 3.780A pdb=" N ASP D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 removed outlier: 4.122A pdb=" N VAL D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE D 442 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 482 removed outlier: 4.169A pdb=" N SER D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 4.511A pdb=" N VAL D 487 " --> pdb=" O MET D 483 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 removed outlier: 4.285A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU D 524 " --> pdb=" O ASN D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 541 removed outlier: 3.591A pdb=" N CYS D 537 " --> pdb=" O ASN D 533 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 541' Processing helix chain 'D' and resid 543 through 551 removed outlier: 4.003A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.705A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 567 " --> pdb=" O VAL D 563 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 4.362A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 572 through 578' Processing helix chain 'D' and resid 579 through 594 removed outlier: 3.665A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 4.128A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP D 601 " --> pdb=" O HIS D 597 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N CYS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 4.115A pdb=" N GLN D 618 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 619 " --> pdb=" O ARG D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 890 removed outlier: 4.148A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA D 883 " --> pdb=" O HIS D 879 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU D 888 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLN D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 935 removed outlier: 5.328A pdb=" N LEU D 935 " --> pdb=" O THR D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 943 through 948 removed outlier: 6.417A pdb=" N GLU D 947 " --> pdb=" O ASP D 943 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP D 948 " --> pdb=" O GLU D 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 943 through 948' Processing helix chain 'D' and resid 956 through 961 Processing helix chain 'D' and resid 978 through 999 removed outlier: 3.973A pdb=" N THR D 982 " --> pdb=" O THR D 978 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 985 " --> pdb=" O GLN D 981 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP D 986 " --> pdb=" O THR D 982 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 987 " --> pdb=" O THR D 983 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP D 999 " --> pdb=" O VAL D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 Processing helix chain 'D' and resid 1030 through 1047 removed outlier: 3.660A pdb=" N ASP D1037 " --> pdb=" O ARG D1033 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR D1045 " --> pdb=" O GLN D1041 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU D1046 " --> pdb=" O ALA D1042 " (cutoff:3.500A) Processing helix chain 'D' and resid 1574 through 1581 removed outlier: 4.145A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET D1579 " --> pdb=" O LEU D1575 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D1581 " --> pdb=" O ALA D1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1574 through 1581' Processing helix chain 'D' and resid 1649 through 1654 removed outlier: 4.112A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1649 through 1654' Processing helix chain 'D' and resid 1656 through 1675 removed outlier: 5.916A pdb=" N GLN D1660 " --> pdb=" O ARG D1656 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG D1661 " --> pdb=" O LEU D1657 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D1674 " --> pdb=" O TYR D1670 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1690 removed outlier: 4.696A pdb=" N ALA D1682 " --> pdb=" O ASN D1678 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP D1690 " --> pdb=" O CYS D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1700 removed outlier: 3.715A pdb=" N LEU D1698 " --> pdb=" O LEU D1694 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1719 removed outlier: 6.764A pdb=" N ARG D1708 " --> pdb=" O PRO D1704 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D1709 " --> pdb=" O GLY D1705 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS D1719 " --> pdb=" O LEU D1715 " (cutoff:3.500A) Processing helix chain 'D' and resid 1720 through 1732 removed outlier: 4.381A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 4.311A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1754 through 1759 removed outlier: 4.437A pdb=" N ARG D1759 " --> pdb=" O GLY D1755 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.826A pdb=" N LEU D1807 " --> pdb=" O PRO D1803 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP D1809 " --> pdb=" O GLU D1805 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU D1812 " --> pdb=" O ARG D1808 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D1819 " --> pdb=" O LEU D1815 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG D1820 " --> pdb=" O GLY D1816 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN D1824 " --> pdb=" O ARG D1820 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix removed outlier: 3.531A pdb=" N MET D1851 " --> pdb=" O THR D1847 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY D1852 " --> pdb=" O LEU D1848 " (cutoff:3.500A) Processing helix chain 'D' and resid 1855 through 1865 removed outlier: 4.355A pdb=" N MET D1865 " --> pdb=" O GLN D1861 " (cutoff:3.500A) Processing helix chain 'D' and resid 1866 through 1871 removed outlier: 3.629A pdb=" N PHE D1871 " --> pdb=" O GLU D1867 " (cutoff:3.500A) Processing helix chain 'D' and resid 1934 through 1984 removed outlier: 4.173A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D1945 " --> pdb=" O ASN D1941 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D1946 " --> pdb=" O LEU D1942 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU D1950 " --> pdb=" O PHE D1946 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D1951 " --> pdb=" O CYS D1947 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D1963 " --> pdb=" O ALA D1959 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG D1964 " --> pdb=" O ALA D1960 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D1975 " --> pdb=" O ALA D1971 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 1999 removed outlier: 4.143A pdb=" N ARG D1996 " --> pdb=" O ALA D1992 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2015 removed outlier: 3.692A pdb=" N LEU D2009 " --> pdb=" O GLN D2005 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D2010 " --> pdb=" O ILE D2006 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS D2011 " --> pdb=" O ASN D2007 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE D2012 " --> pdb=" O MET D2008 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS D2013 " --> pdb=" O LEU D2009 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU D2015 " --> pdb=" O HIS D2011 " (cutoff:3.500A) Processing helix chain 'D' and resid 2027 through 2043 removed outlier: 4.808A pdb=" N LEU D2031 " --> pdb=" O ILE D2027 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D2032 " --> pdb=" O ARG D2028 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY D2043 " --> pdb=" O LEU D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.695A pdb=" N VAL D2103 " --> pdb=" O SER D2099 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.735A pdb=" N VAL D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D2126 " --> pdb=" O SER D2122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2142 Proline residue: D2139 - end of helix removed outlier: 5.688A pdb=" N TYR D2142 " --> pdb=" O LEU D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 3.703A pdb=" N THR D2152 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D2154 " --> pdb=" O GLU D2150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D2155 " --> pdb=" O ASP D2151 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D2161 " --> pdb=" O GLU D2157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D2166 " --> pdb=" O ILE D2162 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2188 removed outlier: 3.703A pdb=" N ASN D2176 " --> pdb=" O PRO D2172 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D2177 " --> pdb=" O GLN D2173 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D2186 " --> pdb=" O ILE D2182 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN D2187 " --> pdb=" O GLY D2183 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN D2188 " --> pdb=" O ASN D2184 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2195 removed outlier: 4.470A pdb=" N GLN D2193 " --> pdb=" O LYS D2189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D2194 " --> pdb=" O VAL D2190 " (cutoff:3.500A) Proline residue: D2195 - end of helix No H-bonds generated for 'chain 'D' and resid 2189 through 2195' Processing helix chain 'D' and resid 2196 through 2202 Processing helix chain 'D' and resid 2203 through 2216 removed outlier: 3.805A pdb=" N ASN D2213 " --> pdb=" O GLU D2209 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D2214 " --> pdb=" O VAL D2210 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D2215 " --> pdb=" O MET D2211 " (cutoff:3.500A) Processing helix chain 'D' and resid 2225 through 2244 removed outlier: 4.719A pdb=" N VAL D2229 " --> pdb=" O PHE D2225 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR D2230 " --> pdb=" O PRO D2226 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER D2231 " --> pdb=" O LYS D2227 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2255 removed outlier: 3.755A pdb=" N SER D2249 " --> pdb=" O GLN D2245 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP D2252 " --> pdb=" O ARG D2248 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER D2255 " --> pdb=" O PHE D2251 " (cutoff:3.500A) Processing helix chain 'D' and resid 2256 through 2265 removed outlier: 3.614A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D2264 " --> pdb=" O ASN D2260 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D2265 " --> pdb=" O SER D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2282 removed outlier: 3.740A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D2276 " --> pdb=" O PRO D2272 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP D2282 " --> pdb=" O ALA D2278 " (cutoff:3.500A) Processing helix chain 'D' and resid 2286 through 2291 removed outlier: 3.595A pdb=" N LEU D2290 " --> pdb=" O LEU D2286 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN D2291 " --> pdb=" O ALA D2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2286 through 2291' Processing helix chain 'D' and resid 2294 through 2309 removed outlier: 3.624A pdb=" N VAL D2299 " --> pdb=" O LEU D2295 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER D2300 " --> pdb=" O GLU D2296 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR D2301 " --> pdb=" O LYS D2297 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D2302 " --> pdb=" O VAL D2298 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D2307 " --> pdb=" O ALA D2303 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER D2309 " --> pdb=" O CYS D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2315 removed outlier: 3.687A pdb=" N LEU D2314 " --> pdb=" O CYS D2310 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2340 removed outlier: 3.501A pdb=" N GLY D2328 " --> pdb=" O ASN D2324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D2330 " --> pdb=" O CYS D2326 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D2331 " --> pdb=" O GLY D2327 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU D2332 " --> pdb=" O GLY D2328 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASP D2333 " --> pdb=" O GLU D2329 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D2335 " --> pdb=" O TYR D2331 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D2337 " --> pdb=" O ASP D2333 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.906A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG D2359 " --> pdb=" O ARG D2355 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2365 through 2370 Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2438 Proline residue: D2438 - end of helix Processing helix chain 'D' and resid 2440 through 2447 removed outlier: 3.634A pdb=" N GLY D2446 " --> pdb=" O LEU D2442 " (cutoff:3.500A) Processing helix chain 'D' and resid 2448 through 2462 removed outlier: 4.154A pdb=" N ARG D2452 " --> pdb=" O GLY D2448 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE D2453 " --> pdb=" O GLU D2449 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2464 through 2472 removed outlier: 3.946A pdb=" N GLY D2468 " --> pdb=" O ASP D2464 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D2469 " --> pdb=" O ASP D2465 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D2471 " --> pdb=" O VAL D2467 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D2472 " --> pdb=" O GLY D2468 " (cutoff:3.500A) Processing helix chain 'D' and resid 2751 through 2774 removed outlier: 4.423A pdb=" N ILE D2755 " --> pdb=" O LEU D2751 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D2758 " --> pdb=" O PHE D2754 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D2759 " --> pdb=" O ILE D2755 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D2762 " --> pdb=" O PHE D2758 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS D2763 " --> pdb=" O ALA D2759 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU D2764 " --> pdb=" O GLU D2760 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS D2765 " --> pdb=" O TYR D2761 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP D2766 " --> pdb=" O THR D2762 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA D2767 " --> pdb=" O HIS D2763 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE D2768 " --> pdb=" O GLU D2764 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP D2769 " --> pdb=" O LYS D2765 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS D2770 " --> pdb=" O TRP D2766 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE D2771 " --> pdb=" O ALA D2767 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN D2772 " --> pdb=" O PHE D2768 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN D2773 " --> pdb=" O ASP D2769 " (cutoff:3.500A) Processing helix chain 'D' and resid 2798 through 2804 removed outlier: 4.916A pdb=" N LYS D2802 " --> pdb=" O SER D2798 " (cutoff:3.500A) Processing helix chain 'D' and resid 2872 through 2896 removed outlier: 5.290A pdb=" N GLU D2876 " --> pdb=" O GLN D2872 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN D2877 " --> pdb=" O ALA D2873 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA D2879 " --> pdb=" O ALA D2875 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN D2881 " --> pdb=" O GLN D2877 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TYR D2882 " --> pdb=" O LEU D2878 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS D2890 " --> pdb=" O TRP D2886 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS D2891 " --> pdb=" O GLY D2887 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN D2892 " --> pdb=" O ARG D2888 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU D2894 " --> pdb=" O LYS D2890 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA D2896 " --> pdb=" O GLN D2892 " (cutoff:3.500A) Processing helix chain 'D' and resid 2919 through 2930 removed outlier: 4.246A pdb=" N ALA D2923 " --> pdb=" O ASP D2919 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU D2925 " --> pdb=" O GLU D2921 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS D2928 " --> pdb=" O GLN D2924 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE D2929 " --> pdb=" O GLU D2925 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D2930 " --> pdb=" O LEU D2926 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3657 removed outlier: 3.668A pdb=" N LEU D3654 " --> pdb=" O CYS D3650 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER D3656 " --> pdb=" O MET D3652 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR D3657 " --> pdb=" O PHE D3653 " (cutoff:3.500A) Processing helix chain 'D' and resid 3668 through 3683 removed outlier: 5.688A pdb=" N ALA D3680 " --> pdb=" O ASP D3676 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY D3681 " --> pdb=" O LEU D3677 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU D3682 " --> pdb=" O SER D3678 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3712 removed outlier: 5.667A pdb=" N GLU D3712 " --> pdb=" O THR D3708 " (cutoff:3.500A) Processing helix chain 'D' and resid 3719 through 3736 removed outlier: 3.516A pdb=" N MET D3723 " --> pdb=" O ASP D3719 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D3727 " --> pdb=" O MET D3723 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER D3732 " --> pdb=" O ILE D3728 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D3736 " --> pdb=" O SER D3732 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3761 Processing helix chain 'D' and resid 3764 through 3771 removed outlier: 4.829A pdb=" N SER D3768 " --> pdb=" O LEU D3764 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS D3771 " --> pdb=" O GLN D3767 " (cutoff:3.500A) Processing helix chain 'D' and resid 3772 through 3787 removed outlier: 3.580A pdb=" N ALA D3776 " --> pdb=" O THR D3772 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU D3777 " --> pdb=" O ARG D3773 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET D3778 " --> pdb=" O GLY D3774 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D3780 " --> pdb=" O ALA D3776 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N CYS D3786 " --> pdb=" O MET D3782 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 3.935A pdb=" N LEU D3805 " --> pdb=" O GLY D3801 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 removed outlier: 3.594A pdb=" N TYR D3819 " --> pdb=" O LYS D3815 " (cutoff:3.500A) Processing helix chain 'D' and resid 3826 through 3839 removed outlier: 7.087A pdb=" N GLN D3830 " --> pdb=" O VAL D3826 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR D3838 " --> pdb=" O ALA D3834 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS D3839 " --> pdb=" O LEU D3835 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3858 removed outlier: 3.659A pdb=" N GLY D3855 " --> pdb=" O ASN D3851 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU D3856 " --> pdb=" O LYS D3852 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY D3857 " --> pdb=" O ALA D3853 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N MET D3858 " --> pdb=" O GLU D3854 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3893 removed outlier: 3.844A pdb=" N ASP D3883 " --> pdb=" O GLU D3879 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU D3893 " --> pdb=" O GLN D3889 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 6.438A pdb=" N GLN D3900 " --> pdb=" O ASN D3896 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN D3901 " --> pdb=" O ASN D3897 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG D3904 " --> pdb=" O GLN D3900 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D3905 " --> pdb=" O ASN D3901 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.597A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP D3935 " --> pdb=" O SER D3931 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR D3936 " --> pdb=" O ASP D3932 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR D3937 " --> pdb=" O PHE D3933 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.694A pdb=" N LYS D3953 " --> pdb=" O ARG D3949 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA D3954 " --> pdb=" O ASN D3950 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET D3955 " --> pdb=" O PHE D3951 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER D3956 " --> pdb=" O SER D3952 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D3957 " --> pdb=" O LYS D3953 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU D3967 " --> pdb=" O ASN D3963 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D3968 " --> pdb=" O SER D3964 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 5.112A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4006 removed outlier: 3.524A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.605A pdb=" N LEU D4013 " --> pdb=" O GLN D4009 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D4030 " --> pdb=" O MET D4026 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU D4032 " --> pdb=" O LEU D4028 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4052 removed outlier: 6.323A pdb=" N ARG D4042 " --> pdb=" O GLY D4038 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN D4043 " --> pdb=" O MET D4039 " (cutoff:3.500A) Processing helix chain 'D' and resid 4053 through 4072 removed outlier: 3.860A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D4065 " --> pdb=" O PHE D4061 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS D4069 " --> pdb=" O PHE D4065 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D4071 " --> pdb=" O LYS D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4081 removed outlier: 5.024A pdb=" N TYR D4080 " --> pdb=" O ALA D4076 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL D4081 " --> pdb=" O PHE D4077 " (cutoff:3.500A) Processing helix chain 'D' and resid 4090 through 4101 removed outlier: 3.715A pdb=" N GLN D4094 " --> pdb=" O LYS D4090 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS D4095 " --> pdb=" O LYS D4091 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D4100 " --> pdb=" O ALA D4096 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 3.826A pdb=" N ILE D4108 " --> pdb=" O THR D4104 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN D4109 " --> pdb=" O GLY D4105 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4137 removed outlier: 5.337A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Proline residue: D4135 - end of helix Processing helix chain 'D' and resid 4138 through 4154 Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 4.187A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D4164 " --> pdb=" O LEU D4160 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU D4165 " --> pdb=" O ARG D4161 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D4166 " --> pdb=" O ASN D4162 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4175 Processing helix chain 'D' and resid 4198 through 4207 removed outlier: 4.073A pdb=" N ARG D4202 " --> pdb=" O SER D4198 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D4204 " --> pdb=" O THR D4200 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4224 removed outlier: 3.540A pdb=" N ASN D4223 " --> pdb=" O PHE D4219 " (cutoff:3.500A) Processing helix chain 'D' and resid 4229 through 4252 removed outlier: 4.174A pdb=" N SER D4252 " --> pdb=" O ALA D4248 " (cutoff:3.500A) Processing helix chain 'D' and resid 4543 through 4559 removed outlier: 4.603A pdb=" N GLN D4547 " --> pdb=" O GLU D4543 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D4557 " --> pdb=" O ASN D4553 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN D4558 " --> pdb=" O TYR D4554 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D4559 " --> pdb=" O LEU D4555 " (cutoff:3.500A) Processing helix chain 'D' and resid 4560 through 4579 removed outlier: 4.225A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4643 through 4684 removed outlier: 3.583A pdb=" N THR D4651 " --> pdb=" O SER D4647 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D4658 " --> pdb=" O ALA D4654 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D4659 " --> pdb=" O PHE D4655 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS D4663 " --> pdb=" O ILE D4659 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix removed outlier: 3.569A pdb=" N ASP D4684 " --> pdb=" O LYS D4680 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4707 removed outlier: 3.584A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4729 removed outlier: 3.505A pdb=" N LEU D4725 " --> pdb=" O LYS D4721 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 removed outlier: 4.424A pdb=" N GLY D4742 " --> pdb=" O ALA D4738 " (cutoff:3.500A) Processing helix chain 'D' and resid 4749 through 4754 Processing helix chain 'D' and resid 4766 through 4771 removed outlier: 4.265A pdb=" N SER D4770 " --> pdb=" O THR D4766 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D4771 " --> pdb=" O TRP D4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4766 through 4771' Processing helix chain 'D' and resid 4772 through 4786 removed outlier: 3.982A pdb=" N ASP D4786 " --> pdb=" O VAL D4782 " (cutoff:3.500A) Processing helix chain 'D' and resid 4787 through 4803 removed outlier: 4.180A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) Processing helix chain 'D' and resid 4807 through 4820 removed outlier: 4.586A pdb=" N ALA D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY D4819 " --> pdb=" O ASP D4815 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL D4820 " --> pdb=" O ILE D4816 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.821A pdb=" N THR D4825 " --> pdb=" O LYS D4821 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D4826 " --> pdb=" O THR D4822 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4858 Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.353A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4897 through 4902 removed outlier: 3.776A pdb=" N ILE D4901 " --> pdb=" O ILE D4897 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4897 through 4902' Processing helix chain 'D' and resid 4909 through 4924 removed outlier: 6.249A pdb=" N VAL D4914 " --> pdb=" O GLU D4910 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL D4915 " --> pdb=" O LEU D4911 " (cutoff:3.500A) Processing helix chain 'D' and resid 4928 through 4957 removed outlier: 3.640A pdb=" N ILE D4936 " --> pdb=" O ILE D4932 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE D4940 " --> pdb=" O ILE D4936 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY D4941 " --> pdb=" O ILE D4937 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D4950 " --> pdb=" O GLN D4946 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS D4951 " --> pdb=" O GLN D4947 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D4955 " --> pdb=" O LYS D4951 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 3.858A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 removed outlier: 6.250A pdb=" N TYR D4988 " --> pdb=" O ASN D4984 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N MET D4989 " --> pdb=" O LEU D4985 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 removed outlier: 3.667A pdb=" N GLU D5016 " --> pdb=" O LYS D5012 " (cutoff:3.500A) Processing helix chain 'D' and resid 5027 through 5033 removed outlier: 6.431A pdb=" N GLN D5031 " --> pdb=" O CYS D5027 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR D5032 " --> pdb=" O PHE D5028 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D5033 " --> pdb=" O ARG D5029 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5027 through 5033' Processing helix chain 'D' and resid 3865 through 3870 removed outlier: 5.590A pdb=" N ARG D3868 " --> pdb=" O VAL D3865 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN D3870 " --> pdb=" O ASN D3867 " (cutoff:3.500A) Processing helix chain 'D' and resid 4685 through 4690 removed outlier: 3.762A pdb=" N GLU D4690 " --> pdb=" O GLY D4685 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4685 through 4690' Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.454A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.639A pdb=" N GLU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.839A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 308 through 313 removed outlier: 6.212A pdb=" N THR B 312 " --> pdb=" O HIS B 308 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.680A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 423 removed outlier: 3.783A pdb=" N ASP B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 removed outlier: 4.101A pdb=" N VAL B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 482 removed outlier: 4.167A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 4.508A pdb=" N VAL B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 removed outlier: 4.282A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 3.583A pdb=" N CYS B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 541' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.971A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.689A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 4.361A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 572 through 578' Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.666A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 4.131A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B 601 " --> pdb=" O HIS B 597 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N CYS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 4.110A pdb=" N GLN B 618 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 890 removed outlier: 4.147A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU B 888 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLN B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 935 removed outlier: 5.262A pdb=" N LEU B 935 " --> pdb=" O THR B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 948 removed outlier: 6.477A pdb=" N GLU B 947 " --> pdb=" O ASP B 943 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 943 through 948' Processing helix chain 'B' and resid 956 through 961 Processing helix chain 'B' and resid 978 through 999 removed outlier: 3.974A pdb=" N THR B 982 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 985 " --> pdb=" O GLN B 981 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 986 " --> pdb=" O THR B 982 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 987 " --> pdb=" O THR B 983 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP B 999 " --> pdb=" O VAL B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1005 Processing helix chain 'B' and resid 1030 through 1047 removed outlier: 3.661A pdb=" N ASP B1037 " --> pdb=" O ARG B1033 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B1045 " --> pdb=" O GLN B1041 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B1046 " --> pdb=" O ALA B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1574 through 1581 removed outlier: 4.125A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET B1579 " --> pdb=" O LEU B1575 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1574 through 1581' Processing helix chain 'B' and resid 1649 through 1654 removed outlier: 4.116A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1649 through 1654' Processing helix chain 'B' and resid 1656 through 1675 removed outlier: 5.913A pdb=" N GLN B1660 " --> pdb=" O ARG B1656 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG B1661 " --> pdb=" O LEU B1657 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B1674 " --> pdb=" O TYR B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1690 removed outlier: 4.698A pdb=" N ALA B1682 " --> pdb=" O ASN B1678 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS B1683 " --> pdb=" O ASN B1679 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP B1690 " --> pdb=" O CYS B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1691 through 1700 removed outlier: 3.686A pdb=" N LEU B1698 " --> pdb=" O LEU B1694 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP B1700 " --> pdb=" O HIS B1696 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1719 removed outlier: 6.752A pdb=" N ARG B1708 " --> pdb=" O PRO B1704 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B1709 " --> pdb=" O GLY B1705 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS B1719 " --> pdb=" O LEU B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1720 through 1732 removed outlier: 4.387A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 4.312A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1759 removed outlier: 4.437A pdb=" N ARG B1759 " --> pdb=" O GLY B1755 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.737A pdb=" N LEU B1807 " --> pdb=" O PRO B1803 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B1809 " --> pdb=" O GLU B1805 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B1812 " --> pdb=" O ARG B1808 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B1819 " --> pdb=" O LEU B1815 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B1820 " --> pdb=" O GLY B1816 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix removed outlier: 3.533A pdb=" N MET B1851 " --> pdb=" O THR B1847 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B1852 " --> pdb=" O LEU B1848 " (cutoff:3.500A) Processing helix chain 'B' and resid 1855 through 1865 removed outlier: 4.333A pdb=" N MET B1865 " --> pdb=" O GLN B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1871 removed outlier: 3.639A pdb=" N PHE B1871 " --> pdb=" O GLU B1867 " (cutoff:3.500A) Processing helix chain 'B' and resid 1934 through 1984 removed outlier: 4.173A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B1950 " --> pdb=" O PHE B1946 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B1951 " --> pdb=" O CYS B1947 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B1964 " --> pdb=" O ALA B1960 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B1975 " --> pdb=" O ALA B1971 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 1999 removed outlier: 4.144A pdb=" N ARG B1996 " --> pdb=" O ALA B1992 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2015 removed outlier: 3.696A pdb=" N LEU B2009 " --> pdb=" O GLN B2005 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B2010 " --> pdb=" O ILE B2006 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B2011 " --> pdb=" O ASN B2007 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B2012 " --> pdb=" O MET B2008 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B2013 " --> pdb=" O LEU B2009 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B2015 " --> pdb=" O HIS B2011 " (cutoff:3.500A) Processing helix chain 'B' and resid 2027 through 2043 removed outlier: 4.809A pdb=" N LEU B2031 " --> pdb=" O ILE B2027 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY B2043 " --> pdb=" O LEU B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.693A pdb=" N VAL B2103 " --> pdb=" O SER B2099 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.736A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B2126 " --> pdb=" O SER B2122 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2142 Proline residue: B2139 - end of helix removed outlier: 5.685A pdb=" N TYR B2142 " --> pdb=" O LEU B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2169 removed outlier: 3.705A pdb=" N THR B2152 " --> pdb=" O SER B2148 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B2154 " --> pdb=" O GLU B2150 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B2155 " --> pdb=" O ASP B2151 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B2166 " --> pdb=" O ILE B2162 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2188 removed outlier: 3.702A pdb=" N ASN B2176 " --> pdb=" O PRO B2172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B2177 " --> pdb=" O GLN B2173 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B2186 " --> pdb=" O ILE B2182 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN B2187 " --> pdb=" O GLY B2183 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASN B2188 " --> pdb=" O ASN B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2195 removed outlier: 4.470A pdb=" N GLN B2193 " --> pdb=" O LYS B2189 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B2194 " --> pdb=" O VAL B2190 " (cutoff:3.500A) Proline residue: B2195 - end of helix No H-bonds generated for 'chain 'B' and resid 2189 through 2195' Processing helix chain 'B' and resid 2196 through 2202 Processing helix chain 'B' and resid 2203 through 2216 removed outlier: 3.794A pdb=" N ASN B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B2215 " --> pdb=" O MET B2211 " (cutoff:3.500A) Processing helix chain 'B' and resid 2225 through 2244 removed outlier: 4.725A pdb=" N VAL B2229 " --> pdb=" O PHE B2225 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B2230 " --> pdb=" O PRO B2226 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B2231 " --> pdb=" O LYS B2227 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2255 removed outlier: 3.754A pdb=" N SER B2249 " --> pdb=" O GLN B2245 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B2252 " --> pdb=" O ARG B2248 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER B2255 " --> pdb=" O PHE B2251 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2265 removed outlier: 3.612A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B2264 " --> pdb=" O ASN B2260 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B2265 " --> pdb=" O SER B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2282 removed outlier: 3.750A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B2276 " --> pdb=" O PRO B2272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP B2282 " --> pdb=" O ALA B2278 " (cutoff:3.500A) Processing helix chain 'B' and resid 2286 through 2291 removed outlier: 3.598A pdb=" N LEU B2290 " --> pdb=" O LEU B2286 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN B2291 " --> pdb=" O ALA B2287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2286 through 2291' Processing helix chain 'B' and resid 2294 through 2309 removed outlier: 3.628A pdb=" N VAL B2299 " --> pdb=" O LEU B2295 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER B2300 " --> pdb=" O GLU B2296 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B2301 " --> pdb=" O LYS B2297 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B2302 " --> pdb=" O VAL B2298 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B2307 " --> pdb=" O ALA B2303 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER B2309 " --> pdb=" O CYS B2305 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2315 removed outlier: 3.691A pdb=" N LEU B2314 " --> pdb=" O CYS B2310 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B2315 " --> pdb=" O PRO B2311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2310 through 2315' Processing helix chain 'B' and resid 2324 through 2340 removed outlier: 3.569A pdb=" N ARG B2330 " --> pdb=" O CYS B2326 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B2331 " --> pdb=" O GLY B2327 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU B2332 " --> pdb=" O GLY B2328 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP B2333 " --> pdb=" O GLU B2329 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B2335 " --> pdb=" O TYR B2331 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B2337 " --> pdb=" O ASP B2333 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.852A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG B2359 " --> pdb=" O ARG B2355 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS B2360 " --> pdb=" O LEU B2356 " (cutoff:3.500A) Proline residue: B2361 - end of helix Processing helix chain 'B' and resid 2365 through 2370 Processing helix chain 'B' and resid 2375 through 2390 Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2438 Proline residue: B2438 - end of helix Processing helix chain 'B' and resid 2440 through 2447 removed outlier: 3.640A pdb=" N GLY B2446 " --> pdb=" O LEU B2442 " (cutoff:3.500A) Processing helix chain 'B' and resid 2448 through 2462 removed outlier: 4.137A pdb=" N ARG B2452 " --> pdb=" O GLY B2448 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B2453 " --> pdb=" O GLU B2449 " (cutoff:3.500A) Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2464 through 2472 removed outlier: 3.930A pdb=" N GLY B2468 " --> pdb=" O ASP B2464 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B2469 " --> pdb=" O ASP B2465 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B2471 " --> pdb=" O VAL B2467 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B2472 " --> pdb=" O GLY B2468 " (cutoff:3.500A) Processing helix chain 'B' and resid 2751 through 2774 removed outlier: 4.421A pdb=" N ILE B2755 " --> pdb=" O LEU B2751 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B2758 " --> pdb=" O PHE B2754 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B2759 " --> pdb=" O ILE B2755 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B2762 " --> pdb=" O PHE B2758 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS B2763 " --> pdb=" O ALA B2759 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU B2764 " --> pdb=" O GLU B2760 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS B2765 " --> pdb=" O TYR B2761 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP B2766 " --> pdb=" O THR B2762 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B2767 " --> pdb=" O HIS B2763 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP B2769 " --> pdb=" O LYS B2765 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS B2770 " --> pdb=" O TRP B2766 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE B2771 " --> pdb=" O ALA B2767 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B2772 " --> pdb=" O PHE B2768 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B2773 " --> pdb=" O ASP B2769 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2804 removed outlier: 4.917A pdb=" N LYS B2802 " --> pdb=" O SER B2798 " (cutoff:3.500A) Processing helix chain 'B' and resid 2872 through 2896 removed outlier: 5.870A pdb=" N GLU B2876 " --> pdb=" O GLN B2872 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN B2877 " --> pdb=" O ALA B2873 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA B2879 " --> pdb=" O ALA B2875 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN B2881 " --> pdb=" O GLN B2877 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR B2882 " --> pdb=" O LEU B2878 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B2883 " --> pdb=" O ALA B2879 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B2890 " --> pdb=" O TRP B2886 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LYS B2891 " --> pdb=" O GLY B2887 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN B2892 " --> pdb=" O ARG B2888 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU B2894 " --> pdb=" O LYS B2890 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA B2896 " --> pdb=" O GLN B2892 " (cutoff:3.500A) Processing helix chain 'B' and resid 2919 through 2930 removed outlier: 4.242A pdb=" N ALA B2923 " --> pdb=" O ASP B2919 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU B2925 " --> pdb=" O GLU B2921 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYS B2928 " --> pdb=" O GLN B2924 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B2929 " --> pdb=" O GLU B2925 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B2930 " --> pdb=" O LEU B2926 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3657 removed outlier: 3.670A pdb=" N LEU B3654 " --> pdb=" O CYS B3650 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER B3656 " --> pdb=" O MET B3652 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR B3657 " --> pdb=" O PHE B3653 " (cutoff:3.500A) Processing helix chain 'B' and resid 3668 through 3683 removed outlier: 5.422A pdb=" N ALA B3680 " --> pdb=" O ASP B3676 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY B3681 " --> pdb=" O LEU B3677 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B3682 " --> pdb=" O SER B3678 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3712 removed outlier: 5.659A pdb=" N GLU B3712 " --> pdb=" O THR B3708 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3736 removed outlier: 3.516A pdb=" N MET B3723 " --> pdb=" O ASP B3719 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B3727 " --> pdb=" O MET B3723 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B3732 " --> pdb=" O ILE B3728 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU B3736 " --> pdb=" O SER B3732 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3761 Processing helix chain 'B' and resid 3764 through 3771 removed outlier: 4.831A pdb=" N SER B3768 " --> pdb=" O LEU B3764 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS B3771 " --> pdb=" O GLN B3767 " (cutoff:3.500A) Processing helix chain 'B' and resid 3772 through 3787 removed outlier: 3.586A pdb=" N ALA B3776 " --> pdb=" O THR B3772 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLU B3777 " --> pdb=" O ARG B3773 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET B3778 " --> pdb=" O GLY B3774 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B3786 " --> pdb=" O MET B3782 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 3.935A pdb=" N LEU B3805 " --> pdb=" O GLY B3801 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 removed outlier: 3.596A pdb=" N TYR B3819 " --> pdb=" O LYS B3815 " (cutoff:3.500A) Processing helix chain 'B' and resid 3826 through 3839 removed outlier: 7.092A pdb=" N GLN B3830 " --> pdb=" O VAL B3826 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B3838 " --> pdb=" O ALA B3834 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS B3839 " --> pdb=" O LEU B3835 " (cutoff:3.500A) Processing helix chain 'B' and resid 3843 through 3858 removed outlier: 3.662A pdb=" N GLY B3855 " --> pdb=" O ASN B3851 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B3856 " --> pdb=" O LYS B3852 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY B3857 " --> pdb=" O ALA B3853 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N MET B3858 " --> pdb=" O GLU B3854 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3893 removed outlier: 3.844A pdb=" N ASP B3883 " --> pdb=" O GLU B3879 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B3893 " --> pdb=" O GLN B3889 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 6.439A pdb=" N GLN B3900 " --> pdb=" O ASN B3896 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN B3901 " --> pdb=" O ASN B3897 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B3904 " --> pdb=" O GLN B3900 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B3905 " --> pdb=" O ASN B3901 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.597A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP B3935 " --> pdb=" O SER B3931 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B3936 " --> pdb=" O ASP B3932 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.686A pdb=" N LYS B3953 " --> pdb=" O ARG B3949 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B3954 " --> pdb=" O ASN B3950 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET B3955 " --> pdb=" O PHE B3951 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B3956 " --> pdb=" O SER B3952 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B3957 " --> pdb=" O LYS B3953 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU B3967 " --> pdb=" O ASN B3963 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR B3968 " --> pdb=" O SER B3964 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 5.115A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4006 removed outlier: 3.510A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.580A pdb=" N LEU B4013 " --> pdb=" O GLN B4009 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B4030 " --> pdb=" O MET B4026 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU B4032 " --> pdb=" O LEU B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4052 removed outlier: 6.320A pdb=" N ARG B4042 " --> pdb=" O GLY B4038 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN B4043 " --> pdb=" O MET B4039 " (cutoff:3.500A) Processing helix chain 'B' and resid 4053 through 4072 removed outlier: 3.858A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B4069 " --> pdb=" O PHE B4065 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B4071 " --> pdb=" O LYS B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4081 removed outlier: 5.022A pdb=" N TYR B4080 " --> pdb=" O ALA B4076 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B4081 " --> pdb=" O PHE B4077 " (cutoff:3.500A) Processing helix chain 'B' and resid 4090 through 4101 removed outlier: 3.722A pdb=" N GLN B4094 " --> pdb=" O LYS B4090 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS B4095 " --> pdb=" O LYS B4091 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B4100 " --> pdb=" O ALA B4096 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 3.825A pdb=" N ILE B4108 " --> pdb=" O THR B4104 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B4109 " --> pdb=" O GLY B4105 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4137 removed outlier: 5.340A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Proline residue: B4135 - end of helix Processing helix chain 'B' and resid 4138 through 4154 Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 4.230A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B4164 " --> pdb=" O LEU B4160 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU B4165 " --> pdb=" O ARG B4161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B4166 " --> pdb=" O ASN B4162 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4175 Processing helix chain 'B' and resid 4198 through 4207 removed outlier: 4.075A pdb=" N ARG B4202 " --> pdb=" O SER B4198 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B4204 " --> pdb=" O THR B4200 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N MET B4207 " --> pdb=" O ALA B4203 " (cutoff:3.500A) Processing helix chain 'B' and resid 4208 through 4224 removed outlier: 3.591A pdb=" N ASN B4223 " --> pdb=" O PHE B4219 " (cutoff:3.500A) Processing helix chain 'B' and resid 4229 through 4252 removed outlier: 4.171A pdb=" N SER B4252 " --> pdb=" O ALA B4248 " (cutoff:3.500A) Processing helix chain 'B' and resid 4543 through 4559 removed outlier: 4.603A pdb=" N GLN B4547 " --> pdb=" O GLU B4543 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B4557 " --> pdb=" O ASN B4553 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B4559 " --> pdb=" O LEU B4555 " (cutoff:3.500A) Processing helix chain 'B' and resid 4560 through 4579 removed outlier: 4.210A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4643 through 4684 removed outlier: 3.580A pdb=" N THR B4651 " --> pdb=" O SER B4647 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B4658 " --> pdb=" O ALA B4654 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B4663 " --> pdb=" O ILE B4659 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B4666 " --> pdb=" O ASN B4662 " (cutoff:3.500A) Proline residue: B4667 - end of helix removed outlier: 3.613A pdb=" N ASP B4684 " --> pdb=" O LYS B4680 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4707 removed outlier: 3.573A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4729 removed outlier: 3.508A pdb=" N LEU B4725 " --> pdb=" O LYS B4721 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 removed outlier: 4.371A pdb=" N GLY B4742 " --> pdb=" O ALA B4738 " (cutoff:3.500A) Processing helix chain 'B' and resid 4749 through 4754 Processing helix chain 'B' and resid 4766 through 4771 removed outlier: 4.264A pdb=" N SER B4770 " --> pdb=" O THR B4766 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B4771 " --> pdb=" O TRP B4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4766 through 4771' Processing helix chain 'B' and resid 4772 through 4786 removed outlier: 3.990A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) Processing helix chain 'B' and resid 4787 through 4803 removed outlier: 4.488A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) Processing helix chain 'B' and resid 4807 through 4820 removed outlier: 4.582A pdb=" N ALA B4811 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY B4819 " --> pdb=" O ASP B4815 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL B4820 " --> pdb=" O ILE B4816 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.814A pdb=" N THR B4825 " --> pdb=" O LYS B4821 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B4826 " --> pdb=" O THR B4822 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.715A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4897 through 4902 removed outlier: 3.848A pdb=" N ILE B4901 " --> pdb=" O ILE B4897 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU B4902 " --> pdb=" O GLY B4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4897 through 4902' Processing helix chain 'B' and resid 4909 through 4924 removed outlier: 6.196A pdb=" N VAL B4914 " --> pdb=" O GLU B4910 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B4915 " --> pdb=" O LEU B4911 " (cutoff:3.500A) Processing helix chain 'B' and resid 4928 through 4957 removed outlier: 3.672A pdb=" N ILE B4936 " --> pdb=" O ILE B4932 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE B4940 " --> pdb=" O ILE B4936 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B4941 " --> pdb=" O ILE B4937 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B4950 " --> pdb=" O GLN B4946 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B4951 " --> pdb=" O GLN B4947 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B4955 " --> pdb=" O LYS B4951 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 3.844A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 removed outlier: 6.230A pdb=" N TYR B4988 " --> pdb=" O ASN B4984 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET B4989 " --> pdb=" O LEU B4985 " (cutoff:3.500A) Processing helix chain 'B' and resid 5004 through 5017 removed outlier: 3.688A pdb=" N GLU B5016 " --> pdb=" O LYS B5012 " (cutoff:3.500A) Processing helix chain 'B' and resid 5027 through 5033 removed outlier: 6.428A pdb=" N GLN B5031 " --> pdb=" O CYS B5027 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR B5032 " --> pdb=" O PHE B5028 " (cutoff:3.500A) Processing helix chain 'B' and resid 3865 through 3870 removed outlier: 5.588A pdb=" N ARG B3868 " --> pdb=" O VAL B3865 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN B3870 " --> pdb=" O ASN B3867 " (cutoff:3.500A) Processing helix chain 'B' and resid 4685 through 4690 removed outlier: 3.769A pdb=" N GLU B4690 " --> pdb=" O GLY B4685 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4685 through 4690' Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.073A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 33 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.340A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.692A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.937A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU A 109 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET A 116 " --> pdb=" O HIS A 111 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 148 through 152 Processing sheet with id= 4, first strand: chain 'A' and resid 181 through 184 Processing sheet with id= 5, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.699A pdb=" N ASP A 228 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 250 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS A 230 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 280 through 284 removed outlier: 4.229A pdb=" N LEU A 262 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N HIS A 218 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= 8, first strand: chain 'A' and resid 681 through 686 Processing sheet with id= 9, first strand: chain 'A' and resid 714 through 717 removed outlier: 5.120A pdb=" N HIS A 720 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A 719 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 723 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 726 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 753 through 759 removed outlier: 3.598A pdb=" N GLU A 665 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 829 through 833 removed outlier: 5.288A pdb=" N TYR A 829 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A 836 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 937 through 940 removed outlier: 4.494A pdb=" N GLY A 940 " --> pdb=" O GLY A1050 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY A1050 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1073 through 1077 Processing sheet with id= 14, first strand: chain 'A' and resid 4177 through 4184 removed outlier: 7.770A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.076A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 33 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.692A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 19 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.934A pdb=" N LEU C 108 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU C 109 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET C 116 " --> pdb=" O HIS C 111 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 148 through 152 Processing sheet with id= 18, first strand: chain 'C' and resid 181 through 184 Processing sheet with id= 19, first strand: chain 'C' and resid 228 through 233 removed outlier: 6.724A pdb=" N ASP C 228 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY C 250 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N CYS C 230 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 280 through 284 removed outlier: 4.237A pdb=" N LEU C 262 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS C 218 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'C' and resid 314 through 318 Processing sheet with id= 22, first strand: chain 'C' and resid 681 through 686 Processing sheet with id= 23, first strand: chain 'C' and resid 714 through 717 removed outlier: 5.074A pdb=" N HIS C 720 " --> pdb=" O ASP C 717 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU C 719 " --> pdb=" O VAL C 730 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 723 " --> pdb=" O VAL C 726 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 726 " --> pdb=" O THR C 723 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 753 through 759 removed outlier: 3.552A pdb=" N GLU C 665 " --> pdb=" O LEU C 792 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 829 through 833 removed outlier: 5.295A pdb=" N TYR C 829 " --> pdb=" O VAL C 840 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 836 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 937 through 940 removed outlier: 4.493A pdb=" N GLY C 940 " --> pdb=" O GLY C1050 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY C1050 " --> pdb=" O GLY C 940 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 1073 through 1077 Processing sheet with id= 28, first strand: chain 'C' and resid 4177 through 4184 removed outlier: 7.785A pdb=" N TYR C4177 " --> pdb=" O ILE C4197 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.074A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D 33 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.690A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU D 19 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.941A pdb=" N LEU D 108 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU D 109 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET D 116 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 148 through 152 Processing sheet with id= 32, first strand: chain 'D' and resid 181 through 184 Processing sheet with id= 33, first strand: chain 'D' and resid 228 through 233 removed outlier: 6.717A pdb=" N ASP D 228 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY D 250 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS D 230 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 280 through 284 removed outlier: 4.233A pdb=" N LEU D 262 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS D 218 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 314 through 318 Processing sheet with id= 36, first strand: chain 'D' and resid 681 through 686 Processing sheet with id= 37, first strand: chain 'D' and resid 714 through 717 removed outlier: 5.058A pdb=" N HIS D 720 " --> pdb=" O ASP D 717 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU D 719 " --> pdb=" O VAL D 730 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 723 " --> pdb=" O VAL D 726 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL D 726 " --> pdb=" O THR D 723 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 753 through 759 removed outlier: 3.550A pdb=" N GLU D 665 " --> pdb=" O LEU D 792 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 829 through 833 removed outlier: 5.293A pdb=" N TYR D 829 " --> pdb=" O VAL D 840 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY D 836 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 937 through 940 removed outlier: 4.491A pdb=" N GLY D 940 " --> pdb=" O GLY D1050 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY D1050 " --> pdb=" O GLY D 940 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 1073 through 1077 Processing sheet with id= 42, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 7.783A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.076A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 33 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.691A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.940A pdb=" N LEU B 108 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU B 109 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B 116 " --> pdb=" O HIS B 111 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 148 through 152 Processing sheet with id= 46, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= 47, first strand: chain 'B' and resid 228 through 233 removed outlier: 6.721A pdb=" N ASP B 228 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY B 250 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS B 230 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'B' and resid 280 through 284 removed outlier: 4.225A pdb=" N LEU B 262 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS B 218 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'B' and resid 314 through 318 Processing sheet with id= 50, first strand: chain 'B' and resid 681 through 686 Processing sheet with id= 51, first strand: chain 'B' and resid 714 through 717 removed outlier: 5.050A pdb=" N HIS B 720 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 719 " --> pdb=" O VAL B 730 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 723 " --> pdb=" O VAL B 726 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 726 " --> pdb=" O THR B 723 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'B' and resid 753 through 759 removed outlier: 3.549A pdb=" N GLU B 665 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'B' and resid 829 through 833 removed outlier: 5.286A pdb=" N TYR B 829 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY B 836 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'B' and resid 937 through 940 removed outlier: 4.601A pdb=" N GLY B 940 " --> pdb=" O GLY B1050 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY B1050 " --> pdb=" O GLY B 940 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'B' and resid 1073 through 1077 Processing sheet with id= 56, first strand: chain 'B' and resid 4177 through 4184 removed outlier: 7.772A pdb=" N TYR B4177 " --> pdb=" O ILE B4197 " (cutoff:3.500A) 3942 hydrogen bonds defined for protein. 11778 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: 56.00 Time building geometry restraints manager: 35.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 4.21: 119501 4.21 - 7.25: 0 7.25 - 10.28: 0 10.28 - 13.32: 0 13.32 - 16.36: 4 Warning: very large bond lengths. Bond restraints: 119505 Sorted by residual: bond pdb="C313 POV C5107 " pdb="C314 POV C5107 " ideal model delta sigma weight residual 1.524 16.359 -14.835 2.00e-02 2.50e+03 5.50e+05 bond pdb="C313 POV A5105 " pdb="C314 POV A5105 " ideal model delta sigma weight residual 1.524 16.359 -14.835 2.00e-02 2.50e+03 5.50e+05 bond pdb="C313 POV B5105 " pdb="C314 POV B5105 " ideal model delta sigma weight residual 1.524 16.358 -14.834 2.00e-02 2.50e+03 5.50e+05 bond pdb="C313 POV C5105 " pdb="C314 POV C5105 " ideal model delta sigma weight residual 1.524 16.358 -14.834 2.00e-02 2.50e+03 5.50e+05 bond pdb=" C32 POV A5105 " pdb=" C33 POV A5105 " ideal model delta sigma weight residual 1.518 1.259 0.259 2.00e-02 2.50e+03 1.68e+02 ... (remaining 119500 not shown) Histogram of bond angle deviations from ideal: 22.80 - 45.54: 4 45.54 - 68.28: 0 68.28 - 91.02: 0 91.02 - 113.76: 69779 113.76 - 136.49: 93134 Bond angle restraints: 162917 Sorted by residual: angle pdb="C312 POV C5105 " pdb="C313 POV C5105 " pdb="C314 POV C5105 " ideal model delta sigma weight residual 112.99 22.80 90.19 3.00e+00 1.11e-01 9.04e+02 angle pdb="C312 POV B5105 " pdb="C313 POV B5105 " pdb="C314 POV B5105 " ideal model delta sigma weight residual 112.99 22.81 90.18 3.00e+00 1.11e-01 9.04e+02 angle pdb="C312 POV C5107 " pdb="C313 POV C5107 " pdb="C314 POV C5107 " ideal model delta sigma weight residual 112.99 22.84 90.15 3.00e+00 1.11e-01 9.03e+02 angle pdb="C312 POV A5105 " pdb="C313 POV A5105 " pdb="C314 POV A5105 " ideal model delta sigma weight residual 112.99 22.85 90.14 3.00e+00 1.11e-01 9.03e+02 angle pdb=" O ARG D1618 " pdb=" C ARG D1618 " pdb=" N ARG D1619 " ideal model delta sigma weight residual 123.33 100.89 22.44 1.13e+00 7.83e-01 3.94e+02 ... (remaining 162912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 66631 21.54 - 43.09: 4136 43.09 - 64.63: 447 64.63 - 86.17: 127 86.17 - 107.71: 20 Dihedral angle restraints: 71361 sinusoidal: 23161 harmonic: 48200 Sorted by residual: dihedral pdb=" CB CYS A4876 " pdb=" SG CYS A4876 " pdb=" SG CYS A4882 " pdb=" CB CYS A4882 " ideal model delta sinusoidal sigma weight residual -86.00 -5.48 -80.52 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS C4876 " pdb=" SG CYS C4876 " pdb=" SG CYS C4882 " pdb=" CB CYS C4882 " ideal model delta sinusoidal sigma weight residual -86.00 -5.91 -80.09 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS B4876 " pdb=" SG CYS B4876 " pdb=" SG CYS B4882 " pdb=" CB CYS B4882 " ideal model delta sinusoidal sigma weight residual -86.00 -6.30 -79.70 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 71358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 17319 0.063 - 0.127: 1609 0.127 - 0.190: 78 0.190 - 0.253: 17 0.253 - 0.317: 10 Chirality restraints: 19033 Sorted by residual: chirality pdb=" C4' ACP A5104 " pdb=" C3' ACP A5104 " pdb=" C5' ACP A5104 " pdb=" O4' ACP A5104 " both_signs ideal model delta sigma weight residual False -2.51 -2.20 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C4' ACP C5104 " pdb=" C3' ACP C5104 " pdb=" C5' ACP C5104 " pdb=" O4' ACP C5104 " both_signs ideal model delta sigma weight residual False -2.51 -2.20 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C4' ACP B5104 " pdb=" C3' ACP B5104 " pdb=" C5' ACP B5104 " pdb=" O4' ACP B5104 " both_signs ideal model delta sigma weight residual False -2.51 -2.20 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 19030 not shown) Planarity restraints: 21423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D1618 " 0.094 2.00e-02 2.50e+03 1.66e-01 2.75e+02 pdb=" C ARG D1618 " -0.287 2.00e-02 2.50e+03 pdb=" O ARG D1618 " 0.106 2.00e-02 2.50e+03 pdb=" N ARG D1619 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C1618 " -0.065 2.00e-02 2.50e+03 1.26e-01 1.58e+02 pdb=" C ARG C1618 " 0.218 2.00e-02 2.50e+03 pdb=" O ARG C1618 " -0.079 2.00e-02 2.50e+03 pdb=" N ARG C1619 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B1617 " 0.041 2.00e-02 2.50e+03 8.05e-02 6.48e+01 pdb=" C THR B1617 " -0.139 2.00e-02 2.50e+03 pdb=" O THR B1617 " 0.053 2.00e-02 2.50e+03 pdb=" N ARG B1618 " 0.045 2.00e-02 2.50e+03 ... (remaining 21420 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.64: 10 1.64 - 2.46: 348 2.46 - 3.27: 126019 3.27 - 4.09: 259608 4.09 - 4.90: 456942 Warning: very small nonbonded interaction distances. Nonbonded interactions: 842927 Sorted by model distance: nonbonded pdb=" O LEU A2867 " pdb=" NE2 GLN A2872 " model vdw 0.831 2.520 nonbonded pdb=" C2 POV B5105 " pdb="C314 POV B5105 " model vdw 1.413 3.870 nonbonded pdb=" C2 POV A5105 " pdb="C314 POV A5105 " model vdw 1.413 3.870 nonbonded pdb=" C2 POV C5105 " pdb="C314 POV C5105 " model vdw 1.413 3.870 nonbonded pdb=" C2 POV C5107 " pdb="C314 POV C5107 " model vdw 1.413 3.870 ... (remaining 842922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 622 or (resid 623 and (name N or name CA or nam \ e C or name O or name CB )) or resid 624 through 819 or (resid 820 and (name N o \ r name CA or name C or name O or name CB )) or resid 821 through 1785 or (resid \ 1786 through 1794 and (name N or name CA or name C or name O or name CB )) or re \ sid 1795 through 1796 or (resid 1797 and (name N or name CA or name C or name O \ or name CB )) or resid 1798 through 2875 or (resid 2876 and (name N or name CA o \ r name C or name O or name CB )) or resid 2877 through 5037 or resid 5101 throug \ h 5105)) selection = (chain 'B' and (resid 12 through 622 or (resid 623 and (name N or name CA or nam \ e C or name O or name CB )) or resid 624 through 819 or (resid 820 and (name N o \ r name CA or name C or name O or name CB )) or resid 821 through 1785 or (resid \ 1786 through 1794 and (name N or name CA or name C or name O or name CB )) or re \ sid 1795 through 1796 or (resid 1797 and (name N or name CA or name C or name O \ or name CB )) or resid 1798 through 2815 or (resid 2867 and (name N or name CA o \ r name C or name O or name CB )) or resid 2868 through 5037 or resid 5101 throug \ h 5105)) selection = (chain 'C' and (resid 12 through 622 or (resid 623 and (name N or name CA or nam \ e C or name O or name CB )) or resid 624 through 819 or (resid 820 and (name N o \ r name CA or name C or name O or name CB )) or resid 821 through 1785 or (resid \ 1786 through 1794 and (name N or name CA or name C or name O or name CB )) or re \ sid 1795 through 2815 or (resid 2867 and (name N or name CA or name C or name O \ or name CB )) or resid 2868 through 2875 or (resid 2876 and (name N or name CA o \ r name C or name O or name CB )) or resid 2877 through 5037 or resid 5101 throug \ h 5105)) selection = (chain 'D' and (resid 12 through 2875 or (resid 2876 and (name N or name CA or n \ ame C or name O or name CB )) or resid 2877 through 5037 or resid 5101 through 5 \ 104 or (resid 5105 and (name C2 or name C3 or name C31 or name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C \ 310 or name C311 or name C312 or name C313 or name C314)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.020 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: 0.090 Extract box with map and model: 19.560 Check model and map are aligned: 1.480 Set scattering table: 0.820 Process input model: 261.850 Find NCS groups from input model: 10.170 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 300.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.086 14.835 119505 Z= 4.673 Angle : 0.814 90.191 162917 Z= 0.397 Chirality : 0.038 0.317 19033 Planarity : 0.004 0.166 21423 Dihedral : 13.973 107.713 39989 Min Nonbonded Distance : 0.831 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.38 % Rotamer: Outliers : 0.28 % Allowed : 0.38 % Favored : 99.34 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.07), residues: 12808 helix: 0.95 (0.07), residues: 5664 sheet: -0.11 (0.16), residues: 996 loop : -1.63 (0.07), residues: 6148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1023 time to evaluate : 8.805 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 1049 average time/residue: 0.9214 time to fit residues: 1746.4133 Evaluate side-chains 802 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 789 time to evaluate : 8.724 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.8156 time to fit residues: 31.0059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN A 495 ASN A 582 HIS A 597 HIS ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 GLN ** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 HIS ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1220 GLN A1254 HIS ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 GLN A1702 HIS A1775 HIS ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2184 ASN ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2204 HIS A2420 HIS ** A2441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2884 ASN ** A3667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3704 HIS ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3814 GLN ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3837 GLN ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4100 GLN A4204 GLN A4700 GLN ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4776 GLN ** A4857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS C 156 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 495 ASN ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS C 597 HIS ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 HIS ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 GLN C1220 GLN C1254 HIS ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1693 GLN C1702 HIS C1775 HIS ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2184 ASN ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2204 HIS C2420 HIS ** C2441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2884 ASN ** C3667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3704 HIS ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3781 GLN C3814 GLN ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3837 GLN ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4100 GLN C4204 GLN C4700 GLN ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4776 GLN C4886 HIS ** C4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4984 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 ASN D 495 ASN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 HIS ** D 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN D 658 GLN ** D 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 HIS ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1220 GLN D1254 HIS ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1693 GLN D1702 HIS D1775 HIS ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2184 ASN ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2204 HIS D2420 HIS ** D2441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2884 ASN ** D3667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3704 HIS ** D3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3781 GLN D3814 GLN ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3837 GLN ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4100 GLN D4204 GLN D4700 GLN ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4776 GLN D4886 HIS ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS B 156 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 ASN B 495 ASN ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 658 GLN ** B 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 HIS ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1206 GLN B1220 GLN ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1693 GLN B1702 HIS B1775 HIS ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2204 HIS B2420 HIS ** B2441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2884 ASN ** B3667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3814 GLN ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3837 GLN ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4100 GLN B4204 GLN B4700 GLN ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4776 GLN ** B4857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4886 HIS ** B4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 99 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.055 0.414 119505 Z= 3.532 Angle : 3.051 35.385 162917 Z= 1.549 Chirality : 0.154 0.779 19033 Planarity : 0.020 0.226 21423 Dihedral : 12.220 163.468 17665 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 72.78 Ramachandran Plot: Outliers : 3.09 % Allowed : 18.89 % Favored : 78.01 % Rotamer: Outliers : 12.68 % Allowed : 20.88 % Favored : 66.44 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.62 % Twisted General : 1.24 % 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: -5.74 (0.05), residues: 12808 helix: -3.94 (0.04), residues: 5560 sheet: -2.54 (0.13), residues: 1276 loop : -3.94 (0.06), residues: 5972 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1897 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1274 poor density : 623 time to evaluate : 8.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1274 outliers final: 753 residues processed: 1785 average time/residue: 0.9142 time to fit residues: 2966.4044 Evaluate side-chains 1365 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 753 poor density : 612 time to evaluate : 7.825 Switching outliers to nearest non-outliers outliers start: 753 outliers final: 5 residues processed: 753 average time/residue: 0.8314 time to fit residues: 1198.0032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1702 HIS A1952 GLN A1953 HIS A1972 ASN A2125 HIS A2184 ASN ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2349 ASN ** A2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3667 HIS ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4806 ASN A4857 ASN ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 ASN ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1702 HIS ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1953 HIS C1972 ASN C2125 HIS C2184 ASN ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2349 ASN ** C2441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3667 HIS C3699 HIS ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4806 ASN ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 639 ASN ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 ASN ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN D1220 GLN ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1702 HIS ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1953 HIS D1972 ASN ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2184 ASN ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2349 ASN ** D2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3667 HIS ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4806 ASN ** D4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 963 ASN ** B1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1220 GLN ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1702 HIS ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1953 HIS B1972 ASN B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2184 ASN ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2349 ASN ** B2734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3667 HIS B3704 HIS ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4806 ASN B4857 ASN ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.7287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.055 0.428 119505 Z= 3.516 Angle : 3.060 35.102 162917 Z= 1.556 Chirality : 0.152 0.871 19033 Planarity : 0.020 0.254 21423 Dihedral : 13.358 127.428 17665 Min Nonbonded Distance : 1.214 Molprobity Statistics. All-atom Clashscore : 83.48 Ramachandran Plot: Outliers : 2.78 % Allowed : 29.61 % Favored : 67.61 % Rotamer: Outliers : 20.88 % Allowed : 23.58 % Favored : 55.55 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.77 % Twisted General : 2.85 % 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: -6.71 (0.05), residues: 12808 helix: -4.45 (0.04), residues: 5504 sheet: -3.21 (0.13), residues: 1316 loop : -4.79 (0.06), residues: 5988 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2682 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2097 poor density : 585 time to evaluate : 8.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2097 outliers final: 1291 residues processed: 2577 average time/residue: 0.8940 time to fit residues: 4172.8492 Evaluate side-chains 1914 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1291 poor density : 623 time to evaluate : 7.800 Switching outliers to nearest non-outliers outliers start: 1291 outliers final: 24 residues processed: 1291 average time/residue: 0.8239 time to fit residues: 2025.1249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1645 ASN ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS A2169 GLN A2176 ASN ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1645 ASN C1952 GLN ** C2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS C2169 GLN C2176 ASN ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2260 ASN ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4102 GLN ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN D 647 ASN ** D 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1220 GLN ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN D1952 GLN ** D2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2169 GLN D2176 ASN D2184 ASN ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2260 ASN D2884 ASN ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN B1952 GLN ** B2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2169 GLN B2176 ASN B2184 ASN ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2260 ASN ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.7830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.055 0.435 119505 Z= 3.539 Angle : 3.082 36.413 162917 Z= 1.565 Chirality : 0.153 0.771 19033 Planarity : 0.021 0.284 21423 Dihedral : 13.519 118.941 17665 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 86.80 Ramachandran Plot: Outliers : 2.44 % Allowed : 33.96 % Favored : 63.61 % Rotamer: Outliers : 18.89 % Allowed : 29.14 % Favored : 51.97 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.10 % Twisted General : 3.11 % 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: -7.01 (0.05), residues: 12808 helix: -4.55 (0.04), residues: 5508 sheet: -3.50 (0.13), residues: 1244 loop : -5.08 (0.06), residues: 6056 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2455 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1897 poor density : 558 time to evaluate : 8.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1897 outliers final: 1165 residues processed: 2382 average time/residue: 0.9214 time to fit residues: 3967.6960 Evaluate side-chains 1745 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1165 poor density : 580 time to evaluate : 8.679 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1165 outliers final: 33 residues processed: 1165 average time/residue: 0.8759 time to fit residues: 1934.9280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 543 ASN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 GLN ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1952 GLN ** A2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS A2184 ASN ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 797 HIS ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS C2184 ASN ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2884 ASN ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4162 ASN ** C4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 HIS ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 919 ASN ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1220 GLN ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1645 ASN ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 HIS ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1645 ASN ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.8261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.055 0.441 119505 Z= 3.537 Angle : 3.085 36.700 162917 Z= 1.566 Chirality : 0.153 0.899 19033 Planarity : 0.021 0.313 21423 Dihedral : 13.674 94.814 17665 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 87.40 Ramachandran Plot: Outliers : 2.49 % Allowed : 36.06 % Favored : 61.45 % Rotamer: Outliers : 18.47 % Allowed : 31.19 % Favored : 50.34 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.10 % Twisted General : 3.18 % 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: -7.15 (0.05), residues: 12808 helix: -4.58 (0.04), residues: 5500 sheet: -3.70 (0.13), residues: 1180 loop : -5.21 (0.05), residues: 6128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2406 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1855 poor density : 551 time to evaluate : 8.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1855 outliers final: 1132 residues processed: 2306 average time/residue: 0.9440 time to fit residues: 3916.2612 Evaluate side-chains 1723 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1132 poor density : 591 time to evaluate : 8.750 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1132 outliers final: 30 residues processed: 1132 average time/residue: 0.8407 time to fit residues: 1810.1219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1645 ASN C1952 GLN ** C2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1688 HIS ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2884 ASN ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2184 ASN ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2884 ASN ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.8484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.055 0.437 119505 Z= 3.544 Angle : 3.093 37.298 162917 Z= 1.570 Chirality : 0.153 0.742 19033 Planarity : 0.021 0.349 21423 Dihedral : 13.790 92.761 17665 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 87.44 Ramachandran Plot: Outliers : 2.54 % Allowed : 36.55 % Favored : 60.92 % Rotamer: Outliers : 14.71 % Allowed : 35.73 % Favored : 49.56 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.76 % Twisted General : 3.26 % 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: -7.22 (0.05), residues: 12808 helix: -4.60 (0.04), residues: 5568 sheet: -3.64 (0.14), residues: 1076 loop : -5.30 (0.05), residues: 6164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2028 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1477 poor density : 551 time to evaluate : 8.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1477 outliers final: 850 residues processed: 1959 average time/residue: 1.0026 time to fit residues: 3530.5965 Evaluate side-chains 1424 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 850 poor density : 574 time to evaluate : 8.913 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 850 outliers final: 31 residues processed: 850 average time/residue: 0.8932 time to fit residues: 1436.6632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2884 ASN ** D2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4043 GLN ** D4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2884 ASN ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.8682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.056 0.453 119505 Z= 3.550 Angle : 3.101 37.477 162917 Z= 1.576 Chirality : 0.155 0.743 19033 Planarity : 0.021 0.360 21423 Dihedral : 13.920 91.380 17665 Min Nonbonded Distance : 1.014 Molprobity Statistics. All-atom Clashscore : 88.21 Ramachandran Plot: Outliers : 2.49 % Allowed : 37.28 % Favored : 60.23 % Rotamer: Outliers : 11.38 % Allowed : 38.74 % Favored : 49.88 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.76 % Twisted General : 3.26 % 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: -7.34 (0.05), residues: 12808 helix: -4.63 (0.04), residues: 5560 sheet: -3.75 (0.13), residues: 1088 loop : -5.42 (0.05), residues: 6160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1143 poor density : 549 time to evaluate : 8.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1143 outliers final: 637 residues processed: 1631 average time/residue: 0.9600 time to fit residues: 2813.0013 Evaluate side-chains 1197 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 637 poor density : 560 time to evaluate : 8.801 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 637 outliers final: 28 residues processed: 637 average time/residue: 0.8809 time to fit residues: 1062.1698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1645 ASN ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2884 ASN ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4043 GLN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 536 ASN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2884 ASN ** C2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2884 ASN ** D2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN B 536 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2884 ASN ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4997 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.8882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.056 0.441 119505 Z= 3.554 Angle : 3.110 37.611 162917 Z= 1.580 Chirality : 0.155 0.737 19033 Planarity : 0.021 0.366 21423 Dihedral : 14.079 91.010 17665 Min Nonbonded Distance : 1.008 Molprobity Statistics. All-atom Clashscore : 88.19 Ramachandran Plot: Outliers : 2.45 % Allowed : 37.73 % Favored : 59.82 % Rotamer: Outliers : 9.46 % Allowed : 40.67 % Favored : 49.87 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.24 % Twisted General : 3.58 % 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: -7.35 (0.05), residues: 12808 helix: -4.66 (0.03), residues: 5600 sheet: -3.80 (0.13), residues: 1096 loop : -5.40 (0.05), residues: 6112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1502 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 950 poor density : 552 time to evaluate : 8.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 950 outliers final: 541 residues processed: 1466 average time/residue: 0.9330 time to fit residues: 2473.4841 Evaluate side-chains 1105 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 541 poor density : 564 time to evaluate : 8.769 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 541 outliers final: 29 residues processed: 541 average time/residue: 0.8429 time to fit residues: 872.3209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4102 GLN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 520 ASN D 536 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1952 GLN ** D2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2884 ASN ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1130 GLN ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2884 ASN ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4997 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.8990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.056 0.440 119505 Z= 3.554 Angle : 3.112 37.631 162917 Z= 1.582 Chirality : 0.155 0.741 19033 Planarity : 0.022 0.372 21423 Dihedral : 14.150 91.116 17665 Min Nonbonded Distance : 1.033 Molprobity Statistics. All-atom Clashscore : 88.55 Ramachandran Plot: Outliers : 2.35 % Allowed : 37.65 % Favored : 60.00 % Rotamer: Outliers : 6.26 % Allowed : 42.60 % Favored : 51.14 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.91 % Twisted General : 3.68 % 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: -7.38 (0.04), residues: 12808 helix: -4.68 (0.03), residues: 5628 sheet: -3.82 (0.13), residues: 1108 loop : -5.43 (0.05), residues: 6072 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 629 poor density : 547 time to evaluate : 8.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 629 outliers final: 323 residues processed: 1139 average time/residue: 0.9685 time to fit residues: 1975.3271 Evaluate side-chains 872 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 549 time to evaluate : 8.809 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 323 outliers final: 28 residues processed: 323 average time/residue: 0.8363 time to fit residues: 522.6379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2884 ASN ** C2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 GLN ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1973 GLN ** D2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1973 GLN ** B2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2884 ASN ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4997 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.9080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.056 0.441 119505 Z= 3.558 Angle : 3.116 37.659 162917 Z= 1.584 Chirality : 0.155 0.820 19033 Planarity : 0.022 0.372 21423 Dihedral : 14.221 91.012 17665 Min Nonbonded Distance : 1.027 Molprobity Statistics. All-atom Clashscore : 88.71 Ramachandran Plot: Outliers : 2.32 % Allowed : 37.98 % Favored : 59.70 % Rotamer: Outliers : 3.56 % Allowed : 43.80 % Favored : 52.64 % Cbeta Deviations : 0.75 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.40 % Twisted General : 3.68 % 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: -7.42 (0.04), residues: 12808 helix: -4.69 (0.03), residues: 5664 sheet: -3.93 (0.13), residues: 1164 loop : -5.45 (0.05), residues: 5980 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25616 Ramachandran restraints generated. 12808 Oldfield, 0 Emsley, 12808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 547 time to evaluate : 8.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 358 outliers final: 194 residues processed: 881 average time/residue: 0.9679 time to fit residues: 1542.3168 Evaluate side-chains 735 residues out of total 11248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 541 time to evaluate : 8.737 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 25 residues processed: 194 average time/residue: 0.8390 time to fit residues: 321.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1973 GLN ** A2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2125 HIS ** A2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 GLN ** C 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1952 GLN C1973 GLN ** C2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2125 HIS ** C2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2884 ASN ** C3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4997 ASN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN ** D 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2125 HIS ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1952 GLN ** B2112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2125 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4043 GLN ** B4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4997 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.088381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.065625 restraints weight = 448622.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.062730 restraints weight = 333576.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.062559 restraints weight = 384529.161| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.9170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.056 0.442 119505 Z= 3.557 Angle : 3.119 37.717 162917 Z= 1.585 Chirality : 0.155 0.779 19033 Planarity : 0.022 0.376 21423 Dihedral : 14.240 91.055 17665 Min Nonbonded Distance : 1.029 Molprobity Statistics. All-atom Clashscore : 88.48 Ramachandran Plot: Outliers : 2.26 % Allowed : 38.22 % Favored : 59.52 % Rotamer: Outliers : 3.85 % Allowed : 43.40 % Favored : 52.75 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.91 % Twisted General : 3.78 % 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: -7.40 (0.04), residues: 12808 helix: -4.69 (0.03), residues: 5628 sheet: -3.80 (0.13), residues: 1096 loop : -5.45 (0.05), residues: 6084 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 66678.04 seconds wall clock time: 1142 minutes 1.79 seconds (68521.79 seconds total)