Starting phenix.real_space_refine on Tue Mar 12 06:12:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dve_27736/03_2024/8dve_27736_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dve_27736/03_2024/8dve_27736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dve_27736/03_2024/8dve_27736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dve_27736/03_2024/8dve_27736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dve_27736/03_2024/8dve_27736_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dve_27736/03_2024/8dve_27736_updated.pdb" } resolution = 3.84 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= 0.003 sd= 0.015 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 4 9.91 5 Zn 4 6.06 5 P 12 5.49 5 S 636 5.16 5 C 73311 2.51 5 N 20488 2.21 5 O 19774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 1652": "OE1" <-> "OE2" Residue "D GLU 1699": "OE1" <-> "OE2" Residue "D GLU 1733": "OE1" <-> "OE2" Residue "D ARG 1743": "NH1" <-> "NH2" Residue "D ARG 2136": "NH1" <-> "NH2" Residue "D ARG 2248": "NH1" <-> "NH2" Residue "D ARG 2330": "NH1" <-> "NH2" Residue "D ARG 2336": "NH1" <-> "NH2" Residue "D PHE 2997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3967": "OE1" <-> "OE2" Residue "D GLU 4232": "OE1" <-> "OE2" Residue "D ARG 4734": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "A ARG 830": "NH1" <-> "NH2" Residue "A GLU 1643": "OE1" <-> "OE2" Residue "A GLU 1652": "OE1" <-> "OE2" Residue "A GLU 1699": "OE1" <-> "OE2" Residue "A ARG 1743": "NH1" <-> "NH2" Residue "A ARG 1993": "NH1" <-> "NH2" Residue "A GLU 2108": "OE1" <-> "OE2" Residue "A GLU 2157": "OE1" <-> "OE2" Residue "A ARG 2248": "NH1" <-> "NH2" Residue "A ARG 2330": "NH1" <-> "NH2" Residue "A ARG 2336": "NH1" <-> "NH2" Residue "A GLU 2347": "OE1" <-> "OE2" Residue "A ARG 2355": "NH1" <-> "NH2" Residue "A PHE 2959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3928": "OE1" <-> "OE2" Residue "A GLU 3967": "OE1" <-> "OE2" Residue "A PHE 4093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G ARG 1141": "NH1" <-> "NH2" Residue "G GLU 1596": "OE1" <-> "OE2" Residue "G ARG 1743": "NH1" <-> "NH2" Residue "G ARG 2248": "NH1" <-> "NH2" Residue "G GLU 2285": "OE1" <-> "OE2" Residue "G ARG 2330": "NH1" <-> "NH2" Residue "G ARG 2336": "NH1" <-> "NH2" Residue "G ARG 2355": "NH1" <-> "NH2" Residue "G GLU 3928": "OE1" <-> "OE2" Residue "G ARG 3949": "NH1" <-> "NH2" Residue "G GLU 4232": "OE1" <-> "OE2" Residue "G ARG 4824": "NH1" <-> "NH2" Residue "G GLU 4955": "OE1" <-> "OE2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "J ARG 275": "NH1" <-> "NH2" Residue "J GLU 509": "OE1" <-> "OE2" Residue "J ARG 830": "NH1" <-> "NH2" Residue "J ARG 1271": "NH1" <-> "NH2" Residue "J GLU 1643": "OE1" <-> "OE2" Residue "J GLU 1652": "OE1" <-> "OE2" Residue "J GLU 1733": "OE1" <-> "OE2" Residue "J ARG 1743": "NH1" <-> "NH2" Residue "J GLU 2157": "OE1" <-> "OE2" Residue "J ARG 2248": "NH1" <-> "NH2" Residue "J GLU 2292": "OE1" <-> "OE2" Residue "J ARG 2336": "NH1" <-> "NH2" Residue "J ARG 2355": "NH1" <-> "NH2" Residue "J GLU 3928": "OE1" <-> "OE2" Residue "J GLU 3967": "OE1" <-> "OE2" Residue "J ARG 4557": "NH1" <-> "NH2" Residue "J ARG 4734": "NH1" <-> "NH2" Residue "J GLU 5000": "OE1" <-> "OE2" Residue "J GLU 5007": "OE1" <-> "OE2" Time to flip residues: 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 114229 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 26818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3942, 26818 Classifications: {'peptide': 3942} Incomplete info: {'truncation_to_alanine': 1348} Link IDs: {'PTRANS': 173, 'TRANS': 3768} Chain breaks: 44 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 4907 Unresolved non-hydrogen angles: 6144 Unresolved non-hydrogen dihedrals: 3945 Unresolved non-hydrogen chiralities: 309 Planarities with less than four sites: {'GLN:plan1': 81, 'ASP:plan': 148, 'TYR:plan': 23, 'ASN:plan1': 54, 'TRP:plan': 12, 'HIS:plan': 26, 'PHE:plan': 25, 'GLU:plan': 283, 'ARG:plan': 111} Unresolved non-hydrogen planarities: 3166 Chain: "E" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 743 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 715 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 469 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 222 Chain: "A" Number of atoms: 27274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3943, 27274 Classifications: {'peptide': 3943} Incomplete info: {'truncation_to_alanine': 1233} Link IDs: {'PTRANS': 173, 'TRANS': 3769} Chain breaks: 44 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 4444 Unresolved non-hydrogen angles: 5575 Unresolved non-hydrogen dihedrals: 3556 Unresolved non-hydrogen chiralities: 278 Planarities with less than four sites: {'GLN:plan1': 67, 'ASP:plan': 140, 'TYR:plan': 21, 'ASN:plan1': 52, 'TRP:plan': 9, 'HIS:plan': 26, 'PHE:plan': 22, 'GLU:plan': 270, 'ARG:plan': 99} Unresolved non-hydrogen planarities: 2909 Chain: "B" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 743 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 720 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 220 Chain: "G" Number of atoms: 27137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3944, 27137 Classifications: {'peptide': 3944} Incomplete info: {'truncation_to_alanine': 1269} Link IDs: {'PTRANS': 173, 'TRANS': 3770} Chain breaks: 44 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 4598 Unresolved non-hydrogen angles: 5771 Unresolved non-hydrogen dihedrals: 3683 Unresolved non-hydrogen chiralities: 291 Planarities with less than four sites: {'GLN:plan1': 73, 'ASP:plan': 141, 'TYR:plan': 24, 'ASN:plan1': 53, 'TRP:plan': 9, 'HIS:plan': 26, 'PHE:plan': 25, 'GLU:plan': 270, 'ARG:plan': 105} Unresolved non-hydrogen planarities: 3008 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 745 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 730 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 214 Chain: "J" Number of atoms: 26962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3943, 26962 Classifications: {'peptide': 3943} Incomplete info: {'truncation_to_alanine': 1305} Link IDs: {'PTRANS': 173, 'TRANS': 3769} Chain breaks: 44 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 4767 Unresolved non-hydrogen angles: 5966 Unresolved non-hydrogen dihedrals: 3842 Unresolved non-hydrogen chiralities: 297 Planarities with less than four sites: {'GLN:plan1': 72, 'ASP:plan': 140, 'TYR:plan': 24, 'ASN:plan1': 52, 'TRP:plan': 11, 'HIS:plan': 25, 'PHE:plan': 27, 'GLU:plan': 269, 'ARG:plan': 117} Unresolved non-hydrogen planarities: 3079 Chain: "K" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 728 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 57 Chain: "L" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 726 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 220 Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 26231 SG CYS D4961 87.887 127.582 144.584 1.00127.04 S ATOM 54927 SG CYS A4958 85.465 139.438 167.955 1.00102.79 S ATOM 54952 SG CYS A4961 88.279 141.670 166.490 1.00 95.61 S ATOM 83531 SG CYS G4958 85.752 162.095 154.840 1.00139.45 S ATOM 83556 SG CYS G4961 88.651 163.304 153.052 1.00129.97 S ATOM A0991 SG CYS J4961 88.439 148.624 129.548 1.00109.98 S ATOM A09NQ SG CYS J5027 91.576 150.008 131.094 1.00107.27 S Time building chain proxies: 43.96, per 1000 atoms: 0.38 Number of scatterers: 114229 At special positions: 0 Unit cell: (212.44, 293.28, 299.86, 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 4 19.99 S 636 16.00 P 12 15.00 O 19774 8.00 N 20488 7.00 C 73311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.04 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS G4876 " - pdb=" SG CYS G4882 " distance=2.03 Simple disulfide: pdb=" SG CYS J4876 " - pdb=" SG CYS J4882 " distance=2.03 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: 34.47 Conformation dependent library (CDL) restraints added in 16.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5104 " pdb="ZN ZN A5104 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5104 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5104 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5104 " - pdb=" SG CYS A4958 " pdb=" ZN D5104 " pdb="ZN ZN D5104 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5104 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5104 " - pdb=" ND1 HIS D4983 " pdb=" ZN G5104 " pdb="ZN ZN G5104 " - pdb=" ND1 HIS G4983 " pdb="ZN ZN G5104 " - pdb=" NE2 HIS G4978 " pdb="ZN ZN G5104 " - pdb=" SG CYS G4958 " pdb="ZN ZN G5104 " - pdb=" SG CYS G4961 " pdb=" ZN J5104 " pdb="ZN ZN J5104 " - pdb=" ND1 HIS J4983 " pdb="ZN ZN J5104 " - pdb=" NE2 HIS J4978 " pdb="ZN ZN J5104 " - pdb=" SG CYS J4961 " pdb="ZN ZN J5104 " - pdb=" SG CYS J5027 " Number of angles added : 5 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31502 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: 686 helices and 81 sheets defined 61.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 58.65 Creating SS restraints... Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.844A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 250 through 256 removed outlier: 4.834A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 256' Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 394 through 422 removed outlier: 4.023A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 Processing helix chain 'D' and resid 460 through 482 removed outlier: 3.573A pdb=" N GLY D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 497 removed outlier: 5.037A pdb=" N TYR D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 508 through 531 removed outlier: 3.943A pdb=" N SER D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D 531 " --> pdb=" O ALA D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 544 removed outlier: 3.761A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 552 removed outlier: 4.315A pdb=" N ASP D 552 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.531A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 4.446A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 3.691A 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: 3.920A pdb=" N GLY D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 4.053A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 Processing helix chain 'D' and resid 810 through 815 removed outlier: 4.269A pdb=" N ALA D 814 " --> pdb=" O PRO D 810 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL D 815 " --> pdb=" O CYS D 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 810 through 815' Processing helix chain 'D' and resid 847 through 853 removed outlier: 4.189A pdb=" N PHE D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) Proline residue: D 853 - end of helix Processing helix chain 'D' and resid 865 through 886 Processing helix chain 'D' and resid 914 through 926 Processing helix chain 'D' and resid 927 through 935 Processing helix chain 'D' and resid 979 through 1004 Processing helix chain 'D' and resid 1028 through 1050 Processing helix chain 'D' and resid 1217 through 1222 removed outlier: 6.815A pdb=" N GLU D1221 " --> pdb=" O CYS D1217 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D1222 " --> pdb=" O GLY D1218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1217 through 1222' Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1444 through 1449 removed outlier: 3.980A pdb=" N VAL D1448 " --> pdb=" O GLU D1444 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TRP D1449 " --> pdb=" O PRO D1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1444 through 1449' Processing helix chain 'D' and resid 1465 through 1470 removed outlier: 5.853A pdb=" N ARG D1470 " --> pdb=" O LEU D1466 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1501 Processing helix chain 'D' and resid 1574 through 1581 removed outlier: 4.059A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU D1581 " --> pdb=" O ALA D1577 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 3.834A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG D1656 " --> pdb=" O GLU D1652 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1649 through 1657' Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.608A pdb=" N CYS D1674 " --> pdb=" O TYR D1670 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1690 removed outlier: 3.869A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D1690 " --> pdb=" O CYS D1686 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1701 removed outlier: 3.843A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D1700 " --> pdb=" O HIS D1696 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA D1701 " --> pdb=" O ALA D1697 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1719 Processing helix chain 'D' and resid 1720 through 1732 removed outlier: 4.108A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 6.079A pdb=" N LEU D1807 " --> pdb=" O PRO D1803 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG D1808 " --> pdb=" O LEU D1804 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP D1809 " --> pdb=" O GLU D1805 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1867 Processing helix chain 'D' and resid 1925 through 1930 removed outlier: 5.414A pdb=" N LYS D1930 " --> pdb=" O LEU D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1932 through 1981 Processing helix chain 'D' and resid 1987 through 2000 removed outlier: 5.227A pdb=" N THR D1991 " --> pdb=" O SER D1987 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER D2000 " --> pdb=" O ARG D1996 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2011 Processing helix chain 'D' and resid 2024 through 2043 removed outlier: 4.090A pdb=" N ASP D2030 " --> pdb=" O ASP D2026 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D2031 " --> pdb=" O ILE D2027 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 4.168A pdb=" N SER D2099 " --> pdb=" O GLN D2095 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.850A 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: 5.461A pdb=" N TYR D2142 " --> pdb=" O LEU D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2148 through 2169 removed outlier: 4.190A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2189 removed outlier: 5.517A pdb=" N LYS D2189 " --> pdb=" O ILE D2185 " (cutoff:3.500A) Processing helix chain 'D' and resid 2190 through 2195 Proline residue: D2195 - end of helix Processing helix chain 'D' and resid 2196 through 2202 Processing helix chain 'D' and resid 2203 through 2216 Processing helix chain 'D' and resid 2225 through 2244 removed outlier: 3.597A pdb=" N VAL D2229 " --> pdb=" O PHE D2225 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2255 removed outlier: 4.493A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N SER D2255 " --> pdb=" O PHE D2251 " (cutoff:3.500A) Processing helix chain 'D' and resid 2256 through 2261 removed outlier: 3.520A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER D2261 " --> pdb=" O LEU D2257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2256 through 2261' Processing helix chain 'D' and resid 2262 through 2268 removed outlier: 4.959A pdb=" N GLN D2268 " --> pdb=" O GLY D2264 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2281 Processing helix chain 'D' and resid 2283 through 2290 Processing helix chain 'D' and resid 2291 through 2309 removed outlier: 4.026A pdb=" N LEU D2295 " --> pdb=" O GLN D2291 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER D2309 " --> pdb=" O CYS D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2310 through 2317 removed outlier: 4.451A pdb=" N LEU D2314 " --> pdb=" O CYS D2310 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2340 removed outlier: 3.699A pdb=" N GLY D2328 " --> pdb=" O ASN D2324 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG D2330 " --> pdb=" O CYS D2326 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D2331 " --> pdb=" O GLY D2327 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D2340 " --> pdb=" O ARG D2336 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 4.280A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2437 removed outlier: 3.882A pdb=" N ALA D2437 " --> pdb=" O LEU D2433 " (cutoff:3.500A) Processing helix chain 'D' and resid 2439 through 2446 Processing helix chain 'D' and resid 2447 through 2462 removed outlier: 3.600A pdb=" N VAL D2461 " --> pdb=" O LEU D2457 " (cutoff:3.500A) Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2463 through 2472 removed outlier: 3.789A pdb=" N VAL D2467 " --> pdb=" O LEU D2463 " (cutoff:3.500A) Processing helix chain 'D' and resid 2489 through 2494 removed outlier: 5.060A pdb=" N PHE D2494 " --> pdb=" O MET D2490 " (cutoff:3.500A) Processing helix chain 'D' and resid 2495 through 2509 removed outlier: 4.224A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2525 Processing helix chain 'D' and resid 2526 through 2538 removed outlier: 4.218A pdb=" N THR D2538 " --> pdb=" O ALA D2534 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2566 removed outlier: 4.015A pdb=" N VAL D2558 " --> pdb=" O LEU D2554 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU D2559 " --> pdb=" O CYS D2555 " (cutoff:3.500A) Proline residue: D2560 - end of helix Processing helix chain 'D' and resid 2575 through 2592 removed outlier: 3.982A pdb=" N VAL D2579 " --> pdb=" O ARG D2575 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR D2587 " --> pdb=" O LEU D2583 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D2588 " --> pdb=" O HIS D2584 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D2591 " --> pdb=" O TYR D2587 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY D2592 " --> pdb=" O ARG D2588 " (cutoff:3.500A) Processing helix chain 'D' and resid 2596 through 2614 removed outlier: 3.507A pdb=" N ILE D2603 " --> pdb=" O GLN D2599 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D2613 " --> pdb=" O ALA D2609 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE D2614 " --> pdb=" O LEU D2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 2615 through 2621 removed outlier: 3.699A pdb=" N GLN D2620 " --> pdb=" O PRO D2616 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS D2621 " --> pdb=" O SER D2617 " (cutoff:3.500A) Processing helix chain 'D' and resid 2622 through 2631 removed outlier: 3.635A pdb=" N PHE D2628 " --> pdb=" O ARG D2624 " (cutoff:3.500A) Proline residue: D2631 - end of helix Processing helix chain 'D' and resid 2636 through 2652 Proline residue: D2640 - end of helix Processing helix chain 'D' and resid 2668 through 2688 removed outlier: 3.814A pdb=" N LEU D2672 " --> pdb=" O SER D2668 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA D2687 " --> pdb=" O PHE D2683 " (cutoff:3.500A) Processing helix chain 'D' and resid 2692 through 2706 Proline residue: D2701 - end of helix Processing helix chain 'D' and resid 2748 through 2774 Processing helix chain 'D' and resid 2793 through 2798 removed outlier: 4.691A pdb=" N SER D2798 " --> pdb=" O TYR D2794 " (cutoff:3.500A) Processing helix chain 'D' and resid 2799 through 2820 Proline residue: D2808 - end of helix Processing helix chain 'D' and resid 2861 through 2866 removed outlier: 4.662A pdb=" N THR D2866 " --> pdb=" O LEU D2862 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2898 removed outlier: 3.558A pdb=" N LYS D2897 " --> pdb=" O GLU D2893 " (cutoff:3.500A) Processing helix chain 'D' and resid 2907 through 2912 removed outlier: 4.679A pdb=" N THR D2912 " --> pdb=" O TYR D2908 " (cutoff:3.500A) Processing helix chain 'D' and resid 2917 through 2934 removed outlier: 3.518A pdb=" N GLU D2921 " --> pdb=" O ALA D2917 " (cutoff:3.500A) Processing helix chain 'D' and resid 2952 through 2979 Processing helix chain 'D' and resid 2992 through 3001 Processing helix chain 'D' and resid 3002 through 3014 Processing helix chain 'D' and resid 3033 through 3050 removed outlier: 3.621A pdb=" N ALA D3047 " --> pdb=" O PHE D3043 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA D3048 " --> pdb=" O CYS D3044 " (cutoff:3.500A) Processing helix chain 'D' and resid 3064 through 3073 removed outlier: 3.826A pdb=" N LEU D3068 " --> pdb=" O VAL D3064 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS D3069 " --> pdb=" O VAL D3065 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE D3070 " --> pdb=" O ASN D3066 " (cutoff:3.500A) Processing helix chain 'D' and resid 3089 through 3111 Processing helix chain 'D' and resid 3127 through 3150 Proline residue: D3138 - end of helix Processing helix chain 'D' and resid 3160 through 3175 removed outlier: 3.863A pdb=" N SER D3164 " --> pdb=" O ASP D3160 " (cutoff:3.500A) Processing helix chain 'D' and resid 3187 through 3199 removed outlier: 3.958A pdb=" N GLY D3191 " --> pdb=" O ARG D3187 " (cutoff:3.500A) Processing helix chain 'D' and resid 3248 through 3257 removed outlier: 3.923A pdb=" N ALA D3257 " --> pdb=" O ILE D3253 " (cutoff:3.500A) Processing helix chain 'D' and resid 3267 through 3284 Proline residue: D3275 - end of helix Proline residue: D3282 - end of helix Processing helix chain 'D' and resid 3309 through 3326 Processing helix chain 'D' and resid 3337 through 3343 removed outlier: 4.195A pdb=" N PHE D3341 " --> pdb=" O ARG D3337 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLN D3343 " --> pdb=" O ALA D3339 " (cutoff:3.500A) Processing helix chain 'D' and resid 3351 through 3379 removed outlier: 5.149A pdb=" N HIS D3355 " --> pdb=" O PRO D3351 " (cutoff:3.500A) Proline residue: D3360 - end of helix removed outlier: 4.184A pdb=" N LEU D3379 " --> pdb=" O GLU D3375 " (cutoff:3.500A) Processing helix chain 'D' and resid 3395 through 3418 removed outlier: 4.297A pdb=" N SER D3399 " --> pdb=" O ARG D3395 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D3408 " --> pdb=" O ASP D3404 " (cutoff:3.500A) Proline residue: D3410 - end of helix Processing helix chain 'D' and resid 3419 through 3427 removed outlier: 4.039A pdb=" N TRP D3423 " --> pdb=" O ASN D3419 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D3426 " --> pdb=" O HIS D3422 " (cutoff:3.500A) Proline residue: D3427 - end of helix Processing helix chain 'D' and resid 3429 through 3449 removed outlier: 3.959A pdb=" N GLU D3433 " --> pdb=" O ALA D3429 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D3448 " --> pdb=" O TYR D3444 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N HIS D3449 " --> pdb=" O TRP D3445 " (cutoff:3.500A) Processing helix chain 'D' and resid 3450 through 3463 removed outlier: 4.044A pdb=" N GLU D3454 " --> pdb=" O ASN D3450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN D3457 " --> pdb=" O ARG D3453 " (cutoff:3.500A) Processing helix chain 'D' and resid 3511 through 3524 Proline residue: D3519 - end of helix removed outlier: 4.399A pdb=" N LEU D3522 " --> pdb=" O LEU D3518 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN D3523 " --> pdb=" O PRO D3519 " (cutoff:3.500A) Processing helix chain 'D' and resid 3529 through 3543 removed outlier: 4.688A pdb=" N ILE D3533 " --> pdb=" O ASP D3529 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET D3534 " --> pdb=" O GLN D3530 " (cutoff:3.500A) Processing helix chain 'D' and resid 3549 through 3555 removed outlier: 4.189A pdb=" N LEU D3553 " --> pdb=" O VAL D3549 " (cutoff:3.500A) Processing helix chain 'D' and resid 3588 through 3611 Processing helix chain 'D' and resid 3628 through 3638 removed outlier: 4.339A pdb=" N PHE D3636 " --> pdb=" O VAL D3632 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG D3637 " --> pdb=" O VAL D3633 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3665 removed outlier: 3.538A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D3663 " --> pdb=" O ALA D3659 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR D3664 " --> pdb=" O ALA D3660 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3679 removed outlier: 3.944A pdb=" N LYS D3679 " --> pdb=" O ASP D3675 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 3.775A pdb=" N MET D3723 " --> pdb=" O ASP D3719 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D3735 " --> pdb=" O LYS D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3772 removed outlier: 3.821A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D3772 " --> pdb=" O SER D3768 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.469A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 Processing helix chain 'D' and resid 3809 through 3824 removed outlier: 3.658A pdb=" N GLN D3813 " --> pdb=" O ASN D3809 " (cutoff:3.500A) Processing helix chain 'D' and resid 3826 through 3840 removed outlier: 5.912A pdb=" N SER D3840 " --> pdb=" O MET D3836 " (cutoff:3.500A) Processing helix chain 'D' and resid 3843 through 3856 removed outlier: 3.675A pdb=" N LEU D3856 " --> pdb=" O LYS D3852 " (cutoff:3.500A) Processing helix chain 'D' and resid 3866 through 3871 removed outlier: 3.543A pdb=" N GLY D3871 " --> pdb=" O ASN D3867 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3893 Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 4.091A pdb=" N ARG D3904 " --> pdb=" O GLN D3900 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR D3905 " --> pdb=" O ASN D3901 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3938 Processing helix chain 'D' and resid 3944 through 3970 Processing helix chain 'D' and resid 3973 through 3983 Processing helix chain 'D' and resid 3984 through 4007 removed outlier: 3.532A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER D4007 " --> pdb=" O LEU D4003 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.694A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D4032 " --> pdb=" O LEU D4028 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4052 Processing helix chain 'D' and resid 4053 through 4075 removed outlier: 3.682A pdb=" N PHE D4065 " --> pdb=" O PHE D4061 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D4066 " --> pdb=" O PHE D4062 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU D4075 " --> pdb=" O ILE D4071 " (cutoff:3.500A) Processing helix chain 'D' and resid 4076 through 4082 removed outlier: 4.731A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 Processing helix chain 'D' and resid 4104 through 4115 Processing helix chain 'D' and resid 4124 through 4137 removed outlier: 4.217A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 3.747A 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: 3.747A pdb=" N GLU D4168 " --> pdb=" O LEU D4164 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4175 removed outlier: 3.738A pdb=" N PHE D4174 " --> pdb=" O ILE D4170 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4207 removed outlier: 3.877A pdb=" N MET D4207 " --> pdb=" O ALA D4203 " (cutoff:3.500A) Processing helix chain 'D' and resid 4208 through 4225 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4324 through 4341 removed outlier: 4.414A pdb=" N ARG D4341 " --> pdb=" O ALA D4337 " (cutoff:3.500A) Processing helix chain 'D' and resid 4541 through 4559 Processing helix chain 'D' and resid 4560 through 4580 removed outlier: 4.682A pdb=" N PHE D4564 " --> pdb=" O TYR D4560 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR D4580 " --> pdb=" O ILE D4576 " (cutoff:3.500A) Processing helix chain 'D' and resid 4640 through 4684 removed outlier: 3.734A pdb=" N SER D4647 " --> pdb=" O LEU D4643 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU D4648 " --> pdb=" O TRP D4644 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix Processing helix chain 'D' and resid 4696 through 4709 removed outlier: 4.517A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR D4708 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Proline residue: D4709 - end of helix Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 5.181A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4734 through 4742 Processing helix chain 'D' and resid 4745 through 4755 removed outlier: 3.569A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS D4753 " --> pdb=" O GLU D4749 " (cutoff:3.500A) Processing helix chain 'D' and resid 4766 through 4772 removed outlier: 4.851A pdb=" N SER D4770 " --> pdb=" O THR D4766 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE D4771 " --> pdb=" O TRP D4767 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASP D4772 " --> pdb=" O LEU D4768 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4766 through 4772' Processing helix chain 'D' and resid 4773 through 4786 Processing helix chain 'D' and resid 4787 through 4806 removed outlier: 3.885A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D4806 " --> pdb=" O GLY D4802 " (cutoff:3.500A) Processing helix chain 'D' and resid 4807 through 4820 removed outlier: 4.713A pdb=" N ALA D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE D4816 " --> pdb=" O HIS D4812 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA D4817 " --> pdb=" O LEU D4813 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.944A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR D4831 " --> pdb=" O LEU D4827 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 removed outlier: 3.638A pdb=" N MET D4839 " --> pdb=" O LYS D4835 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.886A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4902 removed outlier: 4.789A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D4901 " --> pdb=" O ILE D4897 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU D4902 " --> pdb=" O GLY D4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4896 through 4902' Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4928 through 4957 Processing helix chain 'D' and resid 4964 through 4972 removed outlier: 6.241A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP D4969 " --> pdb=" O SER D4965 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR D4971 " --> pdb=" O TYR D4967 " (cutoff:3.500A) Proline residue: D4972 - end of helix No H-bonds generated for 'chain 'D' and resid 4964 through 4972' Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4999 removed outlier: 3.673A pdb=" N TYR D4988 " --> pdb=" O ASN D4984 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET D4989 " --> pdb=" O LEU D4985 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP D4999 " --> pdb=" O LEU D4995 " (cutoff:3.500A) Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5027 through 5033 removed outlier: 3.587A pdb=" N GLU D5033 " --> pdb=" O ARG D5029 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 799 removed outlier: 4.719A pdb=" N GLU D 799 " --> pdb=" O GLY D 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 794 through 799' Processing helix chain 'D' and resid 4685 through 4690 Processing helix chain 'E' and resid 38 through 43 removed outlier: 3.724A pdb=" N ARG E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 67 removed outlier: 4.838A pdb=" N SER E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 removed outlier: 4.252A pdb=" N TYR E 82 " --> pdb=" O PRO E 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.798A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 67 removed outlier: 5.428A pdb=" N SER B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 82 removed outlier: 4.152A pdb=" N TYR B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 3.533A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 67 removed outlier: 4.807A pdb=" N SER H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.824A pdb=" N TYR H 82 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 43 removed outlier: 4.375A pdb=" N ARG K 42 " --> pdb=" O SER K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 67 removed outlier: 5.316A pdb=" N SER K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 removed outlier: 3.696A pdb=" N ALA K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR K 82 " --> pdb=" O PRO K 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 82' Processing helix chain 'F' and resid 1 through 6 removed outlier: 3.692A pdb=" N THR F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 removed outlier: 4.982A pdb=" N ALA F 11 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 56 removed outlier: 3.588A pdb=" N ASP F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 93 removed outlier: 4.423A pdb=" N ASP F 79 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP F 81 " --> pdb=" O MET F 77 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.687A pdb=" N ASN F 112 " --> pdb=" O HIS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 removed outlier: 4.351A pdb=" N ALA F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 148 removed outlier: 3.913A pdb=" N PHE F 142 " --> pdb=" O ASN F 138 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL F 143 " --> pdb=" O TYR F 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 22 removed outlier: 3.789A pdb=" N PHE C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 68 through 89 removed outlier: 4.109A pdb=" N ASP C 79 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.529A pdb=" N ALA C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'I' and resid 6 through 22 removed outlier: 4.101A pdb=" N LYS I 22 " --> pdb=" O SER I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 41 Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 65 through 81 removed outlier: 4.558A pdb=" N ASP I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 95 removed outlier: 3.630A pdb=" N ASP I 94 " --> pdb=" O PHE I 90 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS I 95 " --> pdb=" O ARG I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 113 Processing helix chain 'I' and resid 118 through 129 Processing helix chain 'I' and resid 138 through 148 Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.953A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.703A pdb=" N ASN A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.395A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 256' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 394 through 422 removed outlier: 3.568A pdb=" N SER A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 Processing helix chain 'A' and resid 460 through 482 Processing helix chain 'A' and resid 483 through 497 removed outlier: 4.772A pdb=" N TYR A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 508 through 531 removed outlier: 3.708A pdb=" N SER A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 542 removed outlier: 3.565A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N THR A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.643A pdb=" N VAL A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.203A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.258A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.944A 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: 3.972A pdb=" N GLY A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.932A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 removed outlier: 4.403A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Proline residue: A 627 - end of helix Processing helix chain 'A' and resid 810 through 815 removed outlier: 4.667A pdb=" N ALA A 814 " --> pdb=" O PRO A 810 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 815' Processing helix chain 'A' and resid 847 through 853 Proline residue: A 853 - end of helix Processing helix chain 'A' and resid 865 through 886 removed outlier: 3.980A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 935 removed outlier: 3.697A pdb=" N ARG A 918 " --> pdb=" O PRO A 914 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 927 " --> pdb=" O GLN A 923 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1004 removed outlier: 4.198A pdb=" N THR A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1050 Processing helix chain 'A' and resid 1207 through 1212 removed outlier: 5.645A pdb=" N ARG A1212 " --> pdb=" O VAL A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 3.525A pdb=" N CYS A1217 " --> pdb=" O PHE A1213 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY A1218 " --> pdb=" O PHE A1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1213 through 1218' Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1444 through 1449 removed outlier: 4.017A pdb=" N VAL A1448 " --> pdb=" O GLU A1444 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TRP A1449 " --> pdb=" O PRO A1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1444 through 1449' Processing helix chain 'A' and resid 1465 through 1470 removed outlier: 5.537A pdb=" N ARG A1470 " --> pdb=" O LEU A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1501 removed outlier: 4.292A pdb=" N PHE A1500 " --> pdb=" O TRP A1496 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1496 through 1501' Processing helix chain 'A' and resid 1574 through 1581 removed outlier: 3.842A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 3.890A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1657' Processing helix chain 'A' and resid 1658 through 1675 Processing helix chain 'A' and resid 1678 through 1690 removed outlier: 3.801A pdb=" N ASP A1690 " --> pdb=" O CYS A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1700 Processing helix chain 'A' and resid 1704 through 1719 Processing helix chain 'A' and resid 1720 through 1734 removed outlier: 4.290A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU A1733 " --> pdb=" O SER A1729 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR A1734 " --> pdb=" O MET A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.599A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 6.142A pdb=" N LEU A1807 " --> pdb=" O PRO A1803 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A1808 " --> pdb=" O LEU A1804 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A1809 " --> pdb=" O GLU A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1855 through 1868 Proline residue: A1868 - end of helix Processing helix chain 'A' and resid 1925 through 1930 removed outlier: 5.778A pdb=" N LYS A1930 " --> pdb=" O LEU A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1984 removed outlier: 3.622A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 2000 removed outlier: 3.919A pdb=" N THR A1991 " --> pdb=" O SER A1987 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A1992 " --> pdb=" O ALA A1988 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A2000 " --> pdb=" O ARG A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2011 removed outlier: 3.962A pdb=" N HIS A2011 " --> pdb=" O ASN A2007 " (cutoff:3.500A) Processing helix chain 'A' and resid 2024 through 2043 removed outlier: 3.514A pdb=" N GLY A2043 " --> pdb=" O LEU A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.884A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.757A 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: 5.269A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2169 removed outlier: 3.678A pdb=" N LEU A2165 " --> pdb=" O GLN A2161 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A2166 " --> pdb=" O ILE A2162 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2189 removed outlier: 5.755A pdb=" N LYS A2189 " --> pdb=" O ILE A2185 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2195 Proline residue: A2195 - end of helix Processing helix chain 'A' and resid 2196 through 2202 Processing helix chain 'A' and resid 2203 through 2216 Processing helix chain 'A' and resid 2225 through 2244 removed outlier: 4.058A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2255 removed outlier: 4.105A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER A2255 " --> pdb=" O PHE A2251 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2262 Processing helix chain 'A' and resid 2271 through 2281 removed outlier: 3.513A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2309 removed outlier: 3.883A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A2306 " --> pdb=" O LEU A2302 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A2307 " --> pdb=" O ALA A2303 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN A2308 " --> pdb=" O GLY A2304 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER A2309 " --> pdb=" O CYS A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2317 removed outlier: 3.628A pdb=" N GLY A2317 " --> pdb=" O LEU A2313 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2340 removed outlier: 3.952A pdb=" N ARG A2330 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A2331 " --> pdb=" O GLY A2327 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.834A 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 removed outlier: 5.904A pdb=" N GLY A2370 " --> pdb=" O PRO A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2437 removed outlier: 3.579A pdb=" N ALA A2437 " --> pdb=" O LEU A2433 " (cutoff:3.500A) Processing helix chain 'A' and resid 2439 through 2446 Processing helix chain 'A' and resid 2447 through 2462 Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2463 through 2473 Proline residue: A2473 - end of helix Processing helix chain 'A' and resid 2495 through 2509 removed outlier: 4.234A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2538 removed outlier: 4.910A pdb=" N LEU A2527 " --> pdb=" O ASP A2523 " (cutoff:3.500A) Proline residue: A2528 - end of helix removed outlier: 4.581A pdb=" N THR A2538 " --> pdb=" O ALA A2534 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2566 removed outlier: 3.548A pdb=" N VAL A2558 " --> pdb=" O LEU A2554 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU A2559 " --> pdb=" O CYS A2555 " (cutoff:3.500A) Proline residue: A2560 - end of helix Processing helix chain 'A' and resid 2575 through 2592 removed outlier: 4.304A pdb=" N GLY A2592 " --> pdb=" O ARG A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2596 through 2614 removed outlier: 4.730A pdb=" N TYR A2613 " --> pdb=" O ALA A2609 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE A2614 " --> pdb=" O LEU A2610 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2630 removed outlier: 3.617A pdb=" N LEU A2619 " --> pdb=" O ARG A2615 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A2620 " --> pdb=" O PRO A2616 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS A2621 " --> pdb=" O SER A2617 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU A2622 " --> pdb=" O MET A2618 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE A2628 " --> pdb=" O ARG A2624 " (cutoff:3.500A) Processing helix chain 'A' and resid 2637 through 2652 removed outlier: 3.574A pdb=" N TRP A2652 " --> pdb=" O TYR A2648 " (cutoff:3.500A) Processing helix chain 'A' and resid 2668 through 2689 Processing helix chain 'A' and resid 2693 through 2707 Proline residue: A2701 - end of helix removed outlier: 3.810A pdb=" N ALA A2707 " --> pdb=" O LEU A2703 " (cutoff:3.500A) Processing helix chain 'A' and resid 2749 through 2774 removed outlier: 3.995A pdb=" N SER A2753 " --> pdb=" O GLU A2749 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A2754 " --> pdb=" O LYS A2750 " (cutoff:3.500A) Processing helix chain 'A' and resid 2793 through 2798 removed outlier: 5.190A pdb=" N SER A2798 " --> pdb=" O TYR A2794 " (cutoff:3.500A) Processing helix chain 'A' and resid 2803 through 2820 Proline residue: A2808 - end of helix Processing helix chain 'A' and resid 2868 through 2898 Processing helix chain 'A' and resid 2907 through 2912 removed outlier: 5.069A pdb=" N THR A2912 " --> pdb=" O TYR A2908 " (cutoff:3.500A) Processing helix chain 'A' and resid 2913 through 2934 removed outlier: 4.550A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) Processing helix chain 'A' and resid 2953 through 2978 removed outlier: 4.615A pdb=" N PHE A2957 " --> pdb=" O LYS A2953 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY A2958 " --> pdb=" O ARG A2954 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3014 removed outlier: 4.579A pdb=" N ILE A2995 " --> pdb=" O HIS A2991 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A3002 " --> pdb=" O PHE A2998 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A3003 " --> pdb=" O ALA A2999 " (cutoff:3.500A) Proline residue: A3004 - end of helix Processing helix chain 'A' and resid 3033 through 3052 removed outlier: 4.197A pdb=" N HIS A3052 " --> pdb=" O ALA A3048 " (cutoff:3.500A) Processing helix chain 'A' and resid 3064 through 3073 removed outlier: 3.717A pdb=" N ARG A3073 " --> pdb=" O HIS A3069 " (cutoff:3.500A) Processing helix chain 'A' and resid 3090 through 3111 Processing helix chain 'A' and resid 3127 through 3150 removed outlier: 5.025A pdb=" N TYR A3131 " --> pdb=" O GLN A3127 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A3132 " --> pdb=" O ASN A3128 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A3134 " --> pdb=" O THR A3130 " (cutoff:3.500A) Proline residue: A3138 - end of helix Processing helix chain 'A' and resid 3160 through 3175 removed outlier: 4.397A pdb=" N SER A3164 " --> pdb=" O ASP A3160 " (cutoff:3.500A) Processing helix chain 'A' and resid 3187 through 3199 Processing helix chain 'A' and resid 3249 through 3257 Processing helix chain 'A' and resid 3267 through 3284 Proline residue: A3275 - end of helix Proline residue: A3282 - end of helix Processing helix chain 'A' and resid 3309 through 3326 removed outlier: 3.821A pdb=" N ASN A3313 " --> pdb=" O SER A3309 " (cutoff:3.500A) Processing helix chain 'A' and resid 3337 through 3344 removed outlier: 3.520A pdb=" N PHE A3341 " --> pdb=" O ARG A3337 " (cutoff:3.500A) Proline residue: A3344 - end of helix Processing helix chain 'A' and resid 3351 through 3379 removed outlier: 3.763A pdb=" N HIS A3355 " --> pdb=" O PRO A3351 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A3359 " --> pdb=" O HIS A3355 " (cutoff:3.500A) Proline residue: A3360 - end of helix removed outlier: 3.784A pdb=" N GLU A3375 " --> pdb=" O LYS A3371 " (cutoff:3.500A) Processing helix chain 'A' and resid 3396 through 3421 removed outlier: 3.640A pdb=" N VAL A3400 " --> pdb=" O ASP A3396 " (cutoff:3.500A) Proline residue: A3410 - end of helix removed outlier: 3.975A pdb=" N TYR A3415 " --> pdb=" O LEU A3411 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A3418 " --> pdb=" O ARG A3414 " (cutoff:3.500A) Processing helix chain 'A' and resid 3430 through 3449 removed outlier: 4.327A pdb=" N MET A3437 " --> pdb=" O GLU A3433 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A3438 " --> pdb=" O LEU A3434 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS A3449 " --> pdb=" O TRP A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3463 removed outlier: 4.289A pdb=" N ASN A3457 " --> pdb=" O ARG A3453 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A3458 " --> pdb=" O GLU A3454 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3525 Proline residue: A3519 - end of helix removed outlier: 4.246A pdb=" N LEU A3522 " --> pdb=" O LEU A3518 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN A3523 " --> pdb=" O PRO A3519 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET A3524 " --> pdb=" O ILE A3520 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N CYS A3525 " --> pdb=" O GLY A3521 " (cutoff:3.500A) Processing helix chain 'A' and resid 3530 through 3543 removed outlier: 3.559A pdb=" N MET A3534 " --> pdb=" O GLN A3530 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A3541 " --> pdb=" O LYS A3537 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A3542 " --> pdb=" O THR A3538 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A3543 " --> pdb=" O ARG A3539 " (cutoff:3.500A) Processing helix chain 'A' and resid 3549 through 3554 removed outlier: 3.969A pdb=" N GLN A3554 " --> pdb=" O ARG A3550 " (cutoff:3.500A) Processing helix chain 'A' and resid 3588 through 3611 Processing helix chain 'A' and resid 3625 through 3638 removed outlier: 3.959A pdb=" N PHE A3636 " --> pdb=" O VAL A3632 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG A3637 " --> pdb=" O VAL A3633 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET A3638 " --> pdb=" O ALA A3634 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3645 removed outlier: 3.966A pdb=" N LEU A3644 " --> pdb=" O PRO A3640 " (cutoff:3.500A) Proline residue: A3645 - end of helix No H-bonds generated for 'chain 'A' and resid 3640 through 3645' Processing helix chain 'A' and resid 3646 through 3665 removed outlier: 4.078A pdb=" N ASN A3651 " --> pdb=" O HIS A3647 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE A3662 " --> pdb=" O LYS A3658 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A3663 " --> pdb=" O ALA A3659 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A3664 " --> pdb=" O ALA A3660 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A3665 " --> pdb=" O TRP A3661 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3680 removed outlier: 5.068A pdb=" N ALA A3680 " --> pdb=" O ASP A3676 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 Processing helix chain 'A' and resid 3719 through 3736 removed outlier: 3.567A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A3735 " --> pdb=" O LYS A3731 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A3736 " --> pdb=" O SER A3732 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 removed outlier: 4.089A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A3772 " --> pdb=" O SER A3768 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 3.566A pdb=" N CYS A3786 " --> pdb=" O MET A3782 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 Processing helix chain 'A' and resid 3809 through 3824 removed outlier: 4.202A pdb=" N GLN A3813 " --> pdb=" O ASN A3809 " (cutoff:3.500A) Processing helix chain 'A' and resid 3826 through 3839 Processing helix chain 'A' and resid 3843 through 3856 removed outlier: 3.893A pdb=" N LEU A3856 " --> pdb=" O LYS A3852 " (cutoff:3.500A) Processing helix chain 'A' and resid 3866 through 3871 removed outlier: 3.968A pdb=" N GLY A3871 " --> pdb=" O ASN A3867 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3893 Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 4.261A pdb=" N ARG A3904 " --> pdb=" O GLN A3900 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A3905 " --> pdb=" O ASN A3901 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 4.737A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3945 through 3970 removed outlier: 3.769A pdb=" N ASN A3950 " --> pdb=" O GLN A3946 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 5.396A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4007 removed outlier: 3.814A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER A4007 " --> pdb=" O LEU A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.512A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A4032 " --> pdb=" O LEU A4028 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4052 Processing helix chain 'A' and resid 4053 through 4075 removed outlier: 4.020A pdb=" N LYS A4069 " --> pdb=" O PHE A4065 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A4073 " --> pdb=" O LYS A4069 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU A4075 " --> pdb=" O ILE A4071 " (cutoff:3.500A) Processing helix chain 'A' and resid 4076 through 4081 removed outlier: 3.838A pdb=" N TYR A4080 " --> pdb=" O ALA A4076 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A4081 " --> pdb=" O PHE A4077 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4076 through 4081' Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 3.661A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 5.603A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4137 removed outlier: 4.635A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 4.712A 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 4155 Proline residue: A4155 - end of helix Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 4.035A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A4162 " --> pdb=" O PRO A4158 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A4168 " --> pdb=" O LEU A4164 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4175 Processing helix chain 'A' and resid 4198 through 4207 removed outlier: 4.109A pdb=" N MET A4207 " --> pdb=" O ALA A4203 " (cutoff:3.500A) Processing helix chain 'A' and resid 4208 through 4225 Processing helix chain 'A' and resid 4227 through 4252 removed outlier: 3.980A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4323 through 4341 removed outlier: 3.731A pdb=" N ARG A4341 " --> pdb=" O ALA A4337 " (cutoff:3.500A) Processing helix chain 'A' and resid 4541 through 4559 removed outlier: 4.984A pdb=" N GLU A4545 " --> pdb=" O TRP A4541 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A4546 " --> pdb=" O GLY A4542 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) Processing helix chain 'A' and resid 4560 through 4580 removed outlier: 4.497A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR A4580 " --> pdb=" O ILE A4576 " (cutoff:3.500A) Processing helix chain 'A' and resid 4640 through 4684 removed outlier: 3.561A pdb=" N TRP A4644 " --> pdb=" O GLU A4640 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix Processing helix chain 'A' and resid 4696 through 4707 removed outlier: 3.779A pdb=" N GLN A4700 " --> pdb=" O ASP A4696 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4729 Processing helix chain 'A' and resid 4733 through 4742 removed outlier: 3.739A pdb=" N GLY A4742 " --> pdb=" O ALA A4738 " (cutoff:3.500A) Processing helix chain 'A' and resid 4745 through 4756 removed outlier: 4.232A pdb=" N ILE A4750 " --> pdb=" O ALA A4746 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA A4752 " --> pdb=" O LEU A4748 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N HIS A4753 " --> pdb=" O GLU A4749 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A4756 " --> pdb=" O ALA A4752 " (cutoff:3.500A) Processing helix chain 'A' and resid 4766 through 4771 Processing helix chain 'A' and resid 4772 through 4787 removed outlier: 5.602A pdb=" N ASN A4787 " --> pdb=" O ILE A4783 " (cutoff:3.500A) Processing helix chain 'A' and resid 4788 through 4806 removed outlier: 3.647A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A4806 " --> pdb=" O GLY A4802 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4821 removed outlier: 4.607A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE A4816 " --> pdb=" O HIS A4812 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA A4817 " --> pdb=" O LEU A4813 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS A4821 " --> pdb=" O ALA A4817 " (cutoff:3.500A) Processing helix chain 'A' and resid 4822 through 4833 removed outlier: 3.571A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR A4831 " --> pdb=" O LEU A4827 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4834 through 4858 Processing helix chain 'A' and resid 4859 through 4864 removed outlier: 4.183A pdb=" N TYR A4863 " --> pdb=" O PHE A4859 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASN A4864 " --> pdb=" O ARG A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4859 through 4864' Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 5.006A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4902 removed outlier: 4.831A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A4901 " --> pdb=" O ILE A4897 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU A4902 " --> pdb=" O GLY A4898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4896 through 4902' Processing helix chain 'A' and resid 4909 through 4924 removed outlier: 3.742A pdb=" N PHE A4916 " --> pdb=" O TYR A4912 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4953 Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 3.789A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 removed outlier: 3.894A pdb=" N THR A4977 " --> pdb=" O HIS A4973 " (cutoff:3.500A) Processing helix chain 'A' and resid 4984 through 4999 removed outlier: 5.818A pdb=" N ASP A4999 " --> pdb=" O LEU A4995 " (cutoff:3.500A) Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5027 through 5033 Processing helix chain 'A' and resid 54 through 59 Proline residue: A 59 - end of helix No H-bonds generated for 'chain 'A' and resid 54 through 59' Processing helix chain 'G' and resid 61 through 66 removed outlier: 4.925A pdb=" N CYS G 65 " --> pdb=" O ASP G 61 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N CYS G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 66' Processing helix chain 'G' and resid 74 through 84 removed outlier: 3.631A pdb=" N ASN G 84 " --> pdb=" O GLU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 256 removed outlier: 4.575A pdb=" N THR G 254 " --> pdb=" O GLY G 250 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 313 Processing helix chain 'G' and resid 394 through 423 removed outlier: 3.679A pdb=" N PHE G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 422 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY G 423 " --> pdb=" O ASP G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 453 Processing helix chain 'G' and resid 460 through 482 removed outlier: 3.561A pdb=" N GLY G 482 " --> pdb=" O PHE G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 483 through 497 removed outlier: 4.903A pdb=" N TYR G 497 " --> pdb=" O ARG G 493 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 507 removed outlier: 3.518A pdb=" N TYR G 506 " --> pdb=" O HIS G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 534 removed outlier: 4.012A pdb=" N SER G 514 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU G 517 " --> pdb=" O GLU G 513 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY G 532 " --> pdb=" O SER G 528 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN G 533 " --> pdb=" O LEU G 529 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 535 through 544 removed outlier: 4.435A pdb=" N THR G 542 " --> pdb=" O ALA G 538 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN G 543 " --> pdb=" O LEU G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 552 removed outlier: 4.231A pdb=" N ASP G 552 " --> pdb=" O VAL G 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 556 through 572 removed outlier: 3.842A pdb=" N SER G 571 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Proline residue: G 572 - end of helix Processing helix chain 'G' and resid 573 through 578 removed outlier: 4.457A pdb=" N ILE G 577 " --> pdb=" O GLU G 573 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE G 578 " --> pdb=" O VAL G 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 573 through 578' Processing helix chain 'G' and resid 579 through 594 removed outlier: 4.155A pdb=" N GLY G 594 " --> pdb=" O LEU G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 596 through 609 removed outlier: 4.234A pdb=" N LEU G 600 " --> pdb=" O ASN G 596 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL G 608 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N CYS G 609 " --> pdb=" O SER G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 625 removed outlier: 3.708A pdb=" N LEU G 625 " --> pdb=" O ILE G 621 " (cutoff:3.500A) Processing helix chain 'G' and resid 810 through 815 removed outlier: 4.397A pdb=" N ALA G 814 " --> pdb=" O PRO G 810 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL G 815 " --> pdb=" O CYS G 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 810 through 815' Processing helix chain 'G' and resid 847 through 853 Proline residue: G 853 - end of helix Processing helix chain 'G' and resid 865 through 886 Processing helix chain 'G' and resid 914 through 935 removed outlier: 4.351A pdb=" N ARG G 918 " --> pdb=" O PRO G 914 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU G 927 " --> pdb=" O GLN G 923 " (cutoff:3.500A) Processing helix chain 'G' and resid 979 through 1004 Processing helix chain 'G' and resid 1030 through 1050 Processing helix chain 'G' and resid 1207 through 1212 removed outlier: 3.697A pdb=" N LEU G1211 " --> pdb=" O ASP G1207 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG G1212 " --> pdb=" O VAL G1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1207 through 1212' Processing helix chain 'G' and resid 1213 through 1222 removed outlier: 4.099A pdb=" N GLY G1218 " --> pdb=" O PHE G1214 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU G1219 " --> pdb=" O ALA G1215 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLN G1220 " --> pdb=" O ILE G1216 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU G1221 " --> pdb=" O CYS G1217 " (cutoff:3.500A) Processing helix chain 'G' and resid 1423 through 1430 Processing helix chain 'G' and resid 1444 through 1449 removed outlier: 3.729A pdb=" N VAL G1448 " --> pdb=" O GLU G1444 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP G1449 " --> pdb=" O PRO G1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1444 through 1449' Processing helix chain 'G' and resid 1465 through 1470 removed outlier: 3.521A pdb=" N VAL G1469 " --> pdb=" O ASP G1465 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG G1470 " --> pdb=" O LEU G1466 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1465 through 1470' Processing helix chain 'G' and resid 1496 through 1501 removed outlier: 4.375A pdb=" N PHE G1500 " --> pdb=" O TRP G1496 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL G1501 " --> pdb=" O GLY G1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1496 through 1501' Processing helix chain 'G' and resid 1574 through 1581 removed outlier: 3.821A pdb=" N ALA G1578 " --> pdb=" O PRO G1574 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU G1581 " --> pdb=" O ALA G1577 " (cutoff:3.500A) Processing helix chain 'G' and resid 1649 through 1657 removed outlier: 3.857A pdb=" N LEU G1653 " --> pdb=" O ASP G1649 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N SER G1654 " --> pdb=" O ILE G1650 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU G1655 " --> pdb=" O LEU G1651 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG G1656 " --> pdb=" O GLU G1652 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU G1657 " --> pdb=" O LEU G1653 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1649 through 1657' Processing helix chain 'G' and resid 1658 through 1675 Processing helix chain 'G' and resid 1678 through 1690 removed outlier: 3.681A pdb=" N SER G1687 " --> pdb=" O HIS G1683 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS G1688 " --> pdb=" O ALA G1684 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP G1690 " --> pdb=" O CYS G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1691 through 1700 removed outlier: 3.716A pdb=" N GLU G1699 " --> pdb=" O LEU G1695 " (cutoff:3.500A) Processing helix chain 'G' and resid 1704 through 1719 Processing helix chain 'G' and resid 1720 through 1732 removed outlier: 4.239A pdb=" N SER G1732 " --> pdb=" O ARG G1728 " (cutoff:3.500A) Processing helix chain 'G' and resid 1739 through 1745 removed outlier: 3.544A pdb=" N ILE G1745 " --> pdb=" O GLU G1741 " (cutoff:3.500A) Processing helix chain 'G' and resid 1803 through 1825 removed outlier: 6.276A pdb=" N LEU G1807 " --> pdb=" O PRO G1803 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG G1808 " --> pdb=" O LEU G1804 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP G1809 " --> pdb=" O GLU G1805 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G1812 " --> pdb=" O ARG G1808 " (cutoff:3.500A) Processing helix chain 'G' and resid 1833 through 1852 Proline residue: G1840 - end of helix Processing helix chain 'G' and resid 1855 through 1867 Processing helix chain 'G' and resid 1925 through 1930 removed outlier: 5.457A pdb=" N LYS G1930 " --> pdb=" O LEU G1926 " (cutoff:3.500A) Processing helix chain 'G' and resid 1932 through 1984 removed outlier: 5.658A pdb=" N PHE G1984 " --> pdb=" O LEU G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1987 through 2000 Processing helix chain 'G' and resid 2001 through 2011 Processing helix chain 'G' and resid 2024 through 2043 removed outlier: 3.622A pdb=" N ARG G2028 " --> pdb=" O PRO G2024 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY G2043 " --> pdb=" O LEU G2039 " (cutoff:3.500A) Processing helix chain 'G' and resid 2093 through 2109 removed outlier: 3.752A pdb=" N ASP G2109 " --> pdb=" O TRP G2105 " (cutoff:3.500A) Processing helix chain 'G' and resid 2113 through 2130 removed outlier: 4.075A pdb=" N GLY G2130 " --> pdb=" O ARG G2126 " (cutoff:3.500A) Processing helix chain 'G' and resid 2131 through 2142 Proline residue: G2139 - end of helix removed outlier: 5.401A pdb=" N TYR G2142 " --> pdb=" O LEU G2138 " (cutoff:3.500A) Processing helix chain 'G' and resid 2148 through 2169 removed outlier: 4.196A pdb=" N ILE G2167 " --> pdb=" O ARG G2163 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL G2168 " --> pdb=" O SER G2164 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN G2169 " --> pdb=" O LEU G2165 " (cutoff:3.500A) Processing helix chain 'G' and resid 2171 through 2189 removed outlier: 6.004A pdb=" N LYS G2189 " --> pdb=" O ILE G2185 " (cutoff:3.500A) Processing helix chain 'G' and resid 2190 through 2195 removed outlier: 3.538A pdb=" N HIS G2194 " --> pdb=" O VAL G2190 " (cutoff:3.500A) Proline residue: G2195 - end of helix No H-bonds generated for 'chain 'G' and resid 2190 through 2195' Processing helix chain 'G' and resid 2196 through 2202 removed outlier: 3.803A pdb=" N GLY G2202 " --> pdb=" O MET G2198 " (cutoff:3.500A) Processing helix chain 'G' and resid 2203 through 2216 Processing helix chain 'G' and resid 2225 through 2244 removed outlier: 3.583A pdb=" N VAL G2229 " --> pdb=" O PHE G2225 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER G2243 " --> pdb=" O PHE G2239 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG G2244 " --> pdb=" O CYS G2240 " (cutoff:3.500A) Processing helix chain 'G' and resid 2245 through 2255 removed outlier: 4.340A pdb=" N HIS G2253 " --> pdb=" O SER G2249 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU G2254 " --> pdb=" O MET G2250 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N SER G2255 " --> pdb=" O PHE G2251 " (cutoff:3.500A) Processing helix chain 'G' and resid 2256 through 2263 removed outlier: 4.703A pdb=" N ILE G2263 " --> pdb=" O GLU G2259 " (cutoff:3.500A) Processing helix chain 'G' and resid 2271 through 2281 Processing helix chain 'G' and resid 2283 through 2290 removed outlier: 3.575A pdb=" N ALA G2287 " --> pdb=" O ASN G2283 " (cutoff:3.500A) Processing helix chain 'G' and resid 2291 through 2308 removed outlier: 4.053A pdb=" N LEU G2295 " --> pdb=" O GLN G2291 " (cutoff:3.500A) Processing helix chain 'G' and resid 2310 through 2317 Processing helix chain 'G' and resid 2326 through 2340 removed outlier: 3.935A pdb=" N ARG G2330 " --> pdb=" O CYS G2326 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR G2331 " --> pdb=" O GLY G2327 " (cutoff:3.500A) Processing helix chain 'G' and resid 2346 through 2361 removed outlier: 3.818A pdb=" N VAL G2352 " --> pdb=" O GLU G2348 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G2360 " --> pdb=" O LEU G2356 " (cutoff:3.500A) Proline residue: G2361 - end of helix Processing helix chain 'G' and resid 2365 through 2370 removed outlier: 5.227A pdb=" N GLY G2370 " --> pdb=" O PRO G2366 " (cutoff:3.500A) Processing helix chain 'G' and resid 2375 through 2390 removed outlier: 3.539A pdb=" N ASP G2389 " --> pdb=" O ARG G2385 " (cutoff:3.500A) Proline residue: G2390 - end of helix Processing helix chain 'G' and resid 2417 through 2437 Processing helix chain 'G' and resid 2439 through 2446 Processing helix chain 'G' and resid 2447 through 2462 Proline residue: G2462 - end of helix Processing helix chain 'G' and resid 2463 through 2473 Proline residue: G2473 - end of helix Processing helix chain 'G' and resid 2495 through 2509 removed outlier: 4.193A pdb=" N LYS G2499 " --> pdb=" O VAL G2495 " (cutoff:3.500A) Processing helix chain 'G' and resid 2514 through 2538 removed outlier: 5.297A pdb=" N LEU G2527 " --> pdb=" O ASP G2523 " (cutoff:3.500A) Proline residue: G2528 - end of helix removed outlier: 4.581A pdb=" N THR G2538 " --> pdb=" O ALA G2534 " (cutoff:3.500A) Processing helix chain 'G' and resid 2544 through 2566 removed outlier: 4.639A pdb=" N LEU G2559 " --> pdb=" O CYS G2555 " (cutoff:3.500A) Proline residue: G2560 - end of helix Processing helix chain 'G' and resid 2575 through 2592 removed outlier: 3.560A pdb=" N ARG G2591 " --> pdb=" O TYR G2587 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY G2592 " --> pdb=" O ARG G2588 " (cutoff:3.500A) Processing helix chain 'G' and resid 2596 through 2614 removed outlier: 3.797A pdb=" N TYR G2613 " --> pdb=" O ALA G2609 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE G2614 " --> pdb=" O LEU G2610 " (cutoff:3.500A) Processing helix chain 'G' and resid 2617 through 2627 removed outlier: 4.710A pdb=" N HIS G2621 " --> pdb=" O SER G2617 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU G2622 " --> pdb=" O MET G2618 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG G2625 " --> pdb=" O HIS G2621 " (cutoff:3.500A) Processing helix chain 'G' and resid 2637 through 2652 Processing helix chain 'G' and resid 2668 through 2689 Processing helix chain 'G' and resid 2692 through 2707 Proline residue: G2701 - end of helix removed outlier: 3.576A pdb=" N ALA G2707 " --> pdb=" O LEU G2703 " (cutoff:3.500A) Processing helix chain 'G' and resid 2749 through 2774 removed outlier: 3.995A pdb=" N SER G2753 " --> pdb=" O GLU G2749 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE G2754 " --> pdb=" O LYS G2750 " (cutoff:3.500A) Processing helix chain 'G' and resid 2793 through 2798 removed outlier: 5.190A pdb=" N SER G2798 " --> pdb=" O TYR G2794 " (cutoff:3.500A) Processing helix chain 'G' and resid 2803 through 2820 Proline residue: G2808 - end of helix Processing helix chain 'G' and resid 2868 through 2898 Processing helix chain 'G' and resid 2907 through 2912 removed outlier: 5.070A pdb=" N THR G2912 " --> pdb=" O TYR G2908 " (cutoff:3.500A) Processing helix chain 'G' and resid 2913 through 2934 removed outlier: 4.551A pdb=" N ARG G2918 " --> pdb=" O LYS G2914 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP G2919 " --> pdb=" O GLU G2915 " (cutoff:3.500A) Processing helix chain 'G' and resid 2951 through 2979 Processing helix chain 'G' and resid 2991 through 3014 removed outlier: 4.256A pdb=" N LEU G3002 " --> pdb=" O PHE G2998 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU G3003 " --> pdb=" O ALA G2999 " (cutoff:3.500A) Proline residue: G3004 - end of helix Processing helix chain 'G' and resid 3033 through 3052 removed outlier: 3.944A pdb=" N GLU G3037 " --> pdb=" O ASN G3033 " (cutoff:3.500A) Processing helix chain 'G' and resid 3064 through 3073 removed outlier: 3.819A pdb=" N LEU G3068 " --> pdb=" O VAL G3064 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG G3073 " --> pdb=" O HIS G3069 " (cutoff:3.500A) Processing helix chain 'G' and resid 3089 through 3111 removed outlier: 3.659A pdb=" N ARG G3111 " --> pdb=" O VAL G3107 " (cutoff:3.500A) Processing helix chain 'G' and resid 3127 through 3150 removed outlier: 3.611A pdb=" N TYR G3131 " --> pdb=" O GLN G3127 " (cutoff:3.500A) Proline residue: G3138 - end of helix Processing helix chain 'G' and resid 3160 through 3175 removed outlier: 3.612A pdb=" N SER G3164 " --> pdb=" O ASP G3160 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU G3175 " --> pdb=" O SER G3171 " (cutoff:3.500A) Processing helix chain 'G' and resid 3187 through 3199 removed outlier: 3.772A pdb=" N ALA G3199 " --> pdb=" O ALA G3195 " (cutoff:3.500A) Processing helix chain 'G' and resid 3248 through 3257 removed outlier: 4.621A pdb=" N ASP G3252 " --> pdb=" O ARG G3248 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G3257 " --> pdb=" O ILE G3253 " (cutoff:3.500A) Processing helix chain 'G' and resid 3267 through 3284 Proline residue: G3275 - end of helix Proline residue: G3282 - end of helix Processing helix chain 'G' and resid 3309 through 3326 Processing helix chain 'G' and resid 3337 through 3343 removed outlier: 3.641A pdb=" N PHE G3341 " --> pdb=" O ARG G3337 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN G3343 " --> pdb=" O ALA G3339 " (cutoff:3.500A) Processing helix chain 'G' and resid 3352 through 3379 Proline residue: G3360 - end of helix removed outlier: 3.539A pdb=" N LEU G3379 " --> pdb=" O GLU G3375 " (cutoff:3.500A) Processing helix chain 'G' and resid 3395 through 3421 removed outlier: 3.766A pdb=" N SER G3399 " --> pdb=" O ARG G3395 " (cutoff:3.500A) Proline residue: G3410 - end of helix Processing helix chain 'G' and resid 3430 through 3449 removed outlier: 3.748A pdb=" N LEU G3434 " --> pdb=" O ASN G3430 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET G3437 " --> pdb=" O GLU G3433 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL G3438 " --> pdb=" O LEU G3434 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N HIS G3449 " --> pdb=" O TRP G3445 " (cutoff:3.500A) Processing helix chain 'G' and resid 3450 through 3463 Processing helix chain 'G' and resid 3511 through 3525 Proline residue: G3519 - end of helix removed outlier: 3.959A pdb=" N LEU G3522 " --> pdb=" O LEU G3518 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN G3523 " --> pdb=" O PRO G3519 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS G3525 " --> pdb=" O GLY G3521 " (cutoff:3.500A) Processing helix chain 'G' and resid 3530 through 3543 removed outlier: 3.571A pdb=" N MET G3534 " --> pdb=" O GLN G3530 " (cutoff:3.500A) Processing helix chain 'G' and resid 3549 through 3555 removed outlier: 4.123A pdb=" N ASN G3555 " --> pdb=" O GLU G3551 " (cutoff:3.500A) Processing helix chain 'G' and resid 3588 through 3611 Processing helix chain 'G' and resid 3625 through 3638 removed outlier: 3.673A pdb=" N PHE G3636 " --> pdb=" O VAL G3632 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG G3637 " --> pdb=" O VAL G3633 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET G3638 " --> pdb=" O ALA G3634 " (cutoff:3.500A) Processing helix chain 'G' and resid 3640 through 3645 removed outlier: 3.981A pdb=" N LEU G3644 " --> pdb=" O PRO G3640 " (cutoff:3.500A) Proline residue: G3645 - end of helix No H-bonds generated for 'chain 'G' and resid 3640 through 3645' Processing helix chain 'G' and resid 3646 through 3665 removed outlier: 4.462A pdb=" N ILE G3662 " --> pdb=" O LYS G3658 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU G3663 " --> pdb=" O ALA G3659 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR G3664 " --> pdb=" O ALA G3660 " (cutoff:3.500A) Processing helix chain 'G' and resid 3669 through 3679 removed outlier: 3.736A pdb=" N MET G3673 " --> pdb=" O PHE G3669 " (cutoff:3.500A) Processing helix chain 'G' and resid 3696 through 3711 Processing helix chain 'G' and resid 3719 through 3735 removed outlier: 4.111A pdb=" N HIS G3734 " --> pdb=" O ALA G3730 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G3735 " --> pdb=" O LYS G3731 " (cutoff:3.500A) Processing helix chain 'G' and resid 3752 through 3772 Processing helix chain 'G' and resid 3774 through 3787 removed outlier: 3.524A pdb=" N ILE G3783 " --> pdb=" O VAL G3779 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS G3787 " --> pdb=" O ILE G3783 " (cutoff:3.500A) Processing helix chain 'G' and resid 3791 through 3806 Processing helix chain 'G' and resid 3809 through 3824 removed outlier: 3.502A pdb=" N GLN G3813 " --> pdb=" O ASN G3809 " (cutoff:3.500A) Processing helix chain 'G' and resid 3826 through 3839 Processing helix chain 'G' and resid 3843 through 3857 removed outlier: 3.571A pdb=" N LEU G3856 " --> pdb=" O LYS G3852 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY G3857 " --> pdb=" O ALA G3853 " (cutoff:3.500A) Processing helix chain 'G' and resid 3866 through 3871 Processing helix chain 'G' and resid 3877 through 3893 Processing helix chain 'G' and resid 3896 through 3905 removed outlier: 3.502A pdb=" N GLN G3900 " --> pdb=" O ASN G3896 " (cutoff:3.500A) Processing helix chain 'G' and resid 3914 through 3939 removed outlier: 4.644A pdb=" N CYS G3918 " --> pdb=" O ASN G3914 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLY G3939 " --> pdb=" O TRP G3935 " (cutoff:3.500A) Processing helix chain 'G' and resid 3944 through 3970 Processing helix chain 'G' and resid 3973 through 3984 removed outlier: 5.163A pdb=" N ARG G3984 " --> pdb=" O LEU G3980 " (cutoff:3.500A) Processing helix chain 'G' and resid 3985 through 4007 removed outlier: 3.640A pdb=" N GLN G4005 " --> pdb=" O MET G4001 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP G4006 " --> pdb=" O LYS G4002 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER G4007 " --> pdb=" O LEU G4003 " (cutoff:3.500A) Processing helix chain 'G' and resid 4009 through 4033 removed outlier: 6.086A pdb=" N GLY G4033 " --> pdb=" O SER G4029 " (cutoff:3.500A) Processing helix chain 'G' and resid 4038 through 4052 Processing helix chain 'G' and resid 4053 through 4072 Processing helix chain 'G' and resid 4074 through 4082 removed outlier: 4.042A pdb=" N GLN G4078 " --> pdb=" O SER G4074 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR G4080 " --> pdb=" O ALA G4076 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G4081 " --> pdb=" O PHE G4077 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR G4082 " --> pdb=" O GLN G4078 " (cutoff:3.500A) Processing helix chain 'G' and resid 4089 through 4101 Processing helix chain 'G' and resid 4104 through 4116 removed outlier: 5.436A pdb=" N GLU G4116 " --> pdb=" O LEU G4112 " (cutoff:3.500A) Processing helix chain 'G' and resid 4124 through 4137 removed outlier: 4.634A pdb=" N PHE G4132 " --> pdb=" O PHE G4128 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN G4133 " --> pdb=" O ALA G4129 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU G4134 " --> pdb=" O ASN G4130 " (cutoff:3.500A) Proline residue: G4135 - end of helix Processing helix chain 'G' and resid 4138 through 4155 Proline residue: G4155 - end of helix Processing helix chain 'G' and resid 4157 through 4168 Processing helix chain 'G' and resid 4169 through 4175 Processing helix chain 'G' and resid 4198 through 4207 removed outlier: 3.725A pdb=" N MET G4207 " --> pdb=" O ALA G4203 " (cutoff:3.500A) Processing helix chain 'G' and resid 4208 through 4225 Processing helix chain 'G' and resid 4227 through 4252 removed outlier: 4.763A pdb=" N MET G4231 " --> pdb=" O GLU G4227 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU G4232 " --> pdb=" O ALA G4228 " (cutoff:3.500A) Processing helix chain 'G' and resid 4323 through 4341 Processing helix chain 'G' and resid 4541 through 4559 Processing helix chain 'G' and resid 4560 through 4580 removed outlier: 4.342A pdb=" N PHE G4579 " --> pdb=" O PHE G4575 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR G4580 " --> pdb=" O ILE G4576 " (cutoff:3.500A) Processing helix chain 'G' and resid 4639 through 4684 removed outlier: 3.667A pdb=" N TRP G4644 " --> pdb=" O GLU G4640 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL G4666 " --> pdb=" O ASN G4662 " (cutoff:3.500A) Proline residue: G4667 - end of helix Processing helix chain 'G' and resid 4696 through 4707 removed outlier: 3.504A pdb=" N GLN G4700 " --> pdb=" O ASP G4696 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU G4704 " --> pdb=" O GLN G4700 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL G4705 " --> pdb=" O TRP G4701 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU G4706 " --> pdb=" O ASP G4702 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN G4707 " --> pdb=" O ARG G4703 " (cutoff:3.500A) Processing helix chain 'G' and resid 4719 through 4733 removed outlier: 5.891A pdb=" N ASP G4730 " --> pdb=" O ASP G4726 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE G4731 " --> pdb=" O LYS G4727 " (cutoff:3.500A) Processing helix chain 'G' and resid 4734 through 4742 Processing helix chain 'G' and resid 4745 through 4755 removed outlier: 3.914A pdb=" N ALA G4752 " --> pdb=" O LEU G4748 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS G4753 " --> pdb=" O GLU G4749 " (cutoff:3.500A) Processing helix chain 'G' and resid 4766 through 4772 removed outlier: 5.534A pdb=" N ASP G4772 " --> pdb=" O LEU G4768 " (cutoff:3.500A) Processing helix chain 'G' and resid 4773 through 4787 removed outlier: 5.436A pdb=" N ASN G4787 " --> pdb=" O ILE G4783 " (cutoff:3.500A) Processing helix chain 'G' and resid 4788 through 4806 Processing helix chain 'G' and resid 4807 through 4821 removed outlier: 5.056A pdb=" N ALA G4811 " --> pdb=" O PHE G4807 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS G4812 " --> pdb=" O PHE G4808 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU G4813 " --> pdb=" O PHE G4809 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU G4814 " --> pdb=" O ALA G4810 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASP G4815 " --> pdb=" O ALA G4811 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE G4816 " --> pdb=" O HIS G4812 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA G4817 " --> pdb=" O LEU G4813 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET G4818 " --> pdb=" O LEU G4814 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS G4821 " --> pdb=" O ALA G4817 " (cutoff:3.500A) Processing helix chain 'G' and resid 4822 through 4832 removed outlier: 4.076A pdb=" N VAL G4830 " --> pdb=" O ILE G4826 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR G4831 " --> pdb=" O LEU G4827 " (cutoff:3.500A) Processing helix chain 'G' and resid 4833 through 4859 Processing helix chain 'G' and resid 4878 through 4893 removed outlier: 5.084A pdb=" N VAL G4891 " --> pdb=" O MET G4887 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG G4892 " --> pdb=" O TYR G4888 " (cutoff:3.500A) Processing helix chain 'G' and resid 4909 through 4924 Processing helix chain 'G' and resid 4928 through 4953 Processing helix chain 'G' and resid 4964 through 4970 removed outlier: 4.019A pdb=" N PHE G4968 " --> pdb=" O GLY G4964 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR G4970 " --> pdb=" O ASP G4966 " (cutoff:3.500A) Processing helix chain 'G' and resid 4973 through 4981 removed outlier: 3.758A pdb=" N THR G4977 " --> pdb=" O HIS G4973 " (cutoff:3.500A) Processing helix chain 'G' and resid 4984 through 4999 removed outlier: 5.886A pdb=" N ASP G4999 " --> pdb=" O LEU G4995 " (cutoff:3.500A) Processing helix chain 'G' and resid 5004 through 5017 Processing helix chain 'G' and resid 5027 through 5037 removed outlier: 5.388A pdb=" N ASP G5034 " --> pdb=" O LYS G5030 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLN G5035 " --> pdb=" O GLN G5031 " (cutoff:3.500A) Processing helix chain 'G' and resid 794 through 799 removed outlier: 4.727A pdb=" N GLU G 799 " --> pdb=" O GLY G 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 794 through 799' Processing helix chain 'G' and resid 4685 through 4690 Processing helix chain 'J' and resid 61 through 66 removed outlier: 3.940A pdb=" N CYS J 65 " --> pdb=" O ASP J 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS J 66 " --> pdb=" O LEU J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 66' Processing helix chain 'J' and resid 74 through 84 removed outlier: 3.676A pdb=" N GLN J 79 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 148 removed outlier: 4.812A pdb=" N TRP J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 256 removed outlier: 6.101A pdb=" N CYS J 253 " --> pdb=" O GLY J 249 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR J 254 " --> pdb=" O GLY J 250 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA J 256 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 314 removed outlier: 5.422A pdb=" N PHE J 314 " --> pdb=" O LYS J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 422 Processing helix chain 'J' and resid 437 through 453 Processing helix chain 'J' and resid 460 through 482 removed outlier: 3.635A pdb=" N GLY J 482 " --> pdb=" O PHE J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 483 through 497 removed outlier: 4.573A pdb=" N TYR J 497 " --> pdb=" O ARG J 493 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 507 removed outlier: 3.815A pdb=" N TYR J 506 " --> pdb=" O HIS J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 508 through 531 removed outlier: 4.053A pdb=" N LYS J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU J 517 " --> pdb=" O GLU J 513 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE J 530 " --> pdb=" O LEU J 526 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG J 531 " --> pdb=" O ALA J 527 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 542 removed outlier: 3.741A pdb=" N PHE J 540 " --> pdb=" O ASN J 536 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER J 541 " --> pdb=" O CYS J 537 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N THR J 542 " --> pdb=" O ALA J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 543 through 552 removed outlier: 4.335A pdb=" N ASP J 552 " --> pdb=" O VAL J 548 " (cutoff:3.500A) Processing helix chain 'J' and resid 556 through 571 removed outlier: 3.770A pdb=" N ILE J 560 " --> pdb=" O ALA J 556 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER J 571 " --> pdb=" O VAL J 567 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 578 removed outlier: 4.202A pdb=" N ASN J 576 " --> pdb=" O PRO J 572 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE J 577 " --> pdb=" O GLU J 573 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE J 578 " --> pdb=" O VAL J 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 572 through 578' Processing helix chain 'J' and resid 579 through 594 removed outlier: 3.550A pdb=" N ILE J 583 " --> pdb=" O GLN J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 596 through 609 removed outlier: 4.366A pdb=" N LEU J 600 " --> pdb=" O ASN J 596 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP J 601 " --> pdb=" O HIS J 597 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL J 608 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS J 609 " --> pdb=" O SER J 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 629 removed outlier: 4.171A pdb=" N LEU J 626 " --> pdb=" O THR J 622 " (cutoff:3.500A) Proline residue: J 627 - end of helix Processing helix chain 'J' and resid 810 through 815 removed outlier: 4.564A pdb=" N ALA J 814 " --> pdb=" O PRO J 810 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL J 815 " --> pdb=" O CYS J 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 810 through 815' Processing helix chain 'J' and resid 847 through 853 removed outlier: 3.977A pdb=" N VAL J 852 " --> pdb=" O HIS J 848 " (cutoff:3.500A) Proline residue: J 853 - end of helix Processing helix chain 'J' and resid 868 through 887 removed outlier: 3.851A pdb=" N LYS J 873 " --> pdb=" O ARG J 869 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG J 886 " --> pdb=" O TRP J 882 " (cutoff:3.500A) Processing helix chain 'J' and resid 914 through 935 removed outlier: 3.746A pdb=" N GLU J 927 " --> pdb=" O GLN J 923 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR J 928 " --> pdb=" O MET J 924 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU J 935 " --> pdb=" O THR J 931 " (cutoff:3.500A) Processing helix chain 'J' and resid 980 through 1004 removed outlier: 4.283A pdb=" N LEU J 984 " --> pdb=" O ALA J 980 " (cutoff:3.500A) Processing helix chain 'J' and resid 1028 through 1050 removed outlier: 3.558A pdb=" N THR J1045 " --> pdb=" O GLN J1041 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY J1050 " --> pdb=" O LEU J1046 " (cutoff:3.500A) Processing helix chain 'J' and resid 1213 through 1218 removed outlier: 4.014A pdb=" N GLY J1218 " --> pdb=" O PHE J1214 " (cutoff:3.500A) Processing helix chain 'J' and resid 1423 through 1430 removed outlier: 3.616A pdb=" N LEU J1428 " --> pdb=" O PRO J1424 " (cutoff:3.500A) Processing helix chain 'J' and resid 1444 through 1449 removed outlier: 3.793A pdb=" N VAL J1448 " --> pdb=" O GLU J1444 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TRP J1449 " --> pdb=" O PRO J1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1444 through 1449' Processing helix chain 'J' and resid 1465 through 1470 removed outlier: 5.694A pdb=" N ARG J1470 " --> pdb=" O LEU J1466 " (cutoff:3.500A) Processing helix chain 'J' and resid 1496 through 1501 Processing helix chain 'J' and resid 1574 through 1581 removed outlier: 3.864A pdb=" N ALA J1578 " --> pdb=" O PRO J1574 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU J1581 " --> pdb=" O ALA J1577 " (cutoff:3.500A) Processing helix chain 'J' and resid 1651 through 1657 removed outlier: 4.958A pdb=" N GLU J1655 " --> pdb=" O LEU J1651 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU J1657 " --> pdb=" O LEU J1653 " (cutoff:3.500A) Processing helix chain 'J' and resid 1658 through 1675 Processing helix chain 'J' and resid 1678 through 1690 removed outlier: 3.750A pdb=" N ALA J1684 " --> pdb=" O ARG J1680 " (cutoff:3.500A) Processing helix chain 'J' and resid 1691 through 1700 removed outlier: 4.003A pdb=" N GLU J1699 " --> pdb=" O LEU J1695 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP J1700 " --> pdb=" O HIS J1696 " (cutoff:3.500A) Processing helix chain 'J' and resid 1704 through 1719 Processing helix chain 'J' and resid 1720 through 1731 Processing helix chain 'J' and resid 1739 through 1745 removed outlier: 3.665A pdb=" N ILE J1745 " --> pdb=" O GLU J1741 " (cutoff:3.500A) Processing helix chain 'J' and resid 1803 through 1825 removed outlier: 6.007A pdb=" N LEU J1807 " --> pdb=" O PRO J1803 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG J1808 " --> pdb=" O LEU J1804 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J1809 " --> pdb=" O GLU J1805 " (cutoff:3.500A) Processing helix chain 'J' and resid 1833 through 1852 Proline residue: J1840 - end of helix Processing helix chain 'J' and resid 1855 through 1868 Proline residue: J1868 - end of helix Processing helix chain 'J' and resid 1925 through 1930 removed outlier: 3.681A pdb=" N MET J1929 " --> pdb=" O GLY J1925 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LYS J1930 " --> pdb=" O LEU J1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1925 through 1930' Processing helix chain 'J' and resid 1932 through 1984 removed outlier: 3.547A pdb=" N GLN J1938 " --> pdb=" O SER J1934 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N PHE J1984 " --> pdb=" O LEU J1980 " (cutoff:3.500A) Processing helix chain 'J' and resid 1987 through 1999 removed outlier: 3.824A pdb=" N GLU J1997 " --> pdb=" O ARG J1993 " (cutoff:3.500A) Processing helix chain 'J' and resid 2001 through 2011 removed outlier: 4.062A pdb=" N HIS J2011 " --> pdb=" O ASN J2007 " (cutoff:3.500A) Processing helix chain 'J' and resid 2024 through 2043 removed outlier: 3.754A pdb=" N ARG J2028 " --> pdb=" O PRO J2024 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY J2043 " --> pdb=" O LEU J2039 " (cutoff:3.500A) Processing helix chain 'J' and resid 2093 through 2109 removed outlier: 3.852A pdb=" N ASP J2109 " --> pdb=" O TRP J2105 " (cutoff:3.500A) Processing helix chain 'J' and resid 2113 through 2130 removed outlier: 4.201A pdb=" N GLY J2130 " --> pdb=" O ARG J2126 " (cutoff:3.500A) Processing helix chain 'J' and resid 2131 through 2142 Proline residue: J2139 - end of helix removed outlier: 5.285A pdb=" N TYR J2142 " --> pdb=" O LEU J2138 " (cutoff:3.500A) Processing helix chain 'J' and resid 2148 through 2169 removed outlier: 4.077A pdb=" N ILE J2167 " --> pdb=" O ARG J2163 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL J2168 " --> pdb=" O SER J2164 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN J2169 " --> pdb=" O LEU J2165 " (cutoff:3.500A) Processing helix chain 'J' and resid 2171 through 2189 removed outlier: 5.682A pdb=" N LYS J2189 " --> pdb=" O ILE J2185 " (cutoff:3.500A) Processing helix chain 'J' and resid 2190 through 2195 Proline residue: J2195 - end of helix Processing helix chain 'J' and resid 2196 through 2202 Processing helix chain 'J' and resid 2203 through 2216 Processing helix chain 'J' and resid 2225 through 2244 removed outlier: 4.353A pdb=" N SER J2243 " --> pdb=" O PHE J2239 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG J2244 " --> pdb=" O CYS J2240 " (cutoff:3.500A) Processing helix chain 'J' and resid 2245 through 2255 removed outlier: 4.596A pdb=" N HIS J2253 " --> pdb=" O SER J2249 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU J2254 " --> pdb=" O MET J2250 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER J2255 " --> pdb=" O PHE J2251 " (cutoff:3.500A) Processing helix chain 'J' and resid 2256 through 2263 removed outlier: 4.819A pdb=" N ILE J2263 " --> pdb=" O GLU J2259 " (cutoff:3.500A) Processing helix chain 'J' and resid 2271 through 2281 removed outlier: 3.794A pdb=" N ILE J2281 " --> pdb=" O ALA J2277 " (cutoff:3.500A) Processing helix chain 'J' and resid 2283 through 2290 Processing helix chain 'J' and resid 2291 through 2308 removed outlier: 3.898A pdb=" N LEU J2295 " --> pdb=" O GLN J2291 " (cutoff:3.500A) Processing helix chain 'J' and resid 2310 through 2317 removed outlier: 4.260A pdb=" N LYS J2316 " --> pdb=" O MET J2312 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY J2317 " --> pdb=" O LEU J2313 " (cutoff:3.500A) Processing helix chain 'J' and resid 2326 through 2340 removed outlier: 4.265A pdb=" N ARG J2330 " --> pdb=" O CYS J2326 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR J2331 " --> pdb=" O GLY J2327 " (cutoff:3.500A) Processing helix chain 'J' and resid 2346 through 2361 removed outlier: 3.625A pdb=" N LYS J2360 " --> pdb=" O LEU J2356 " (cutoff:3.500A) Proline residue: J2361 - end of helix Processing helix chain 'J' and resid 2365 through 2370 removed outlier: 5.332A pdb=" N GLY J2370 " --> pdb=" O PRO J2366 " (cutoff:3.500A) Processing helix chain 'J' and resid 2375 through 2390 Proline residue: J2390 - end of helix Processing helix chain 'J' and resid 2417 through 2437 Processing helix chain 'J' and resid 2439 through 2446 Processing helix chain 'J' and resid 2447 through 2462 removed outlier: 3.532A pdb=" N VAL J2461 " --> pdb=" O LEU J2457 " (cutoff:3.500A) Proline residue: J2462 - end of helix Processing helix chain 'J' and resid 2463 through 2472 removed outlier: 3.681A pdb=" N LEU J2472 " --> pdb=" O GLY J2468 " (cutoff:3.500A) Processing helix chain 'J' and resid 2495 through 2509 Processing helix chain 'J' and resid 2514 through 2538 removed outlier: 4.299A pdb=" N PHE J2526 " --> pdb=" O LEU J2522 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU J2527 " --> pdb=" O ASP J2523 " (cutoff:3.500A) Proline residue: J2528 - end of helix removed outlier: 4.436A pdb=" N THR J2538 " --> pdb=" O ALA J2534 " (cutoff:3.500A) Processing helix chain 'J' and resid 2544 through 2566 removed outlier: 3.906A pdb=" N VAL J2558 " --> pdb=" O LEU J2554 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU J2559 " --> pdb=" O CYS J2555 " (cutoff:3.500A) Proline residue: J2560 - end of helix Processing helix chain 'J' and resid 2575 through 2592 removed outlier: 3.514A pdb=" N VAL J2579 " --> pdb=" O ARG J2575 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS J2584 " --> pdb=" O ASP J2580 " (cutoff:3.500A) Processing helix chain 'J' and resid 2596 through 2614 removed outlier: 5.045A pdb=" N TYR J2613 " --> pdb=" O ALA J2609 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE J2614 " --> pdb=" O LEU J2610 " (cutoff:3.500A) Processing helix chain 'J' and resid 2615 through 2631 removed outlier: 4.165A pdb=" N LEU J2619 " --> pdb=" O ARG J2615 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN J2620 " --> pdb=" O PRO J2616 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N HIS J2621 " --> pdb=" O SER J2617 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU J2622 " --> pdb=" O MET J2618 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP J2629 " --> pdb=" O ARG J2625 " (cutoff:3.500A) Proline residue: J2631 - end of helix Processing helix chain 'J' and resid 2637 through 2652 Processing helix chain 'J' and resid 2668 through 2689 Processing helix chain 'J' and resid 2692 through 2707 Proline residue: J2701 - end of helix removed outlier: 4.258A pdb=" N ALA J2707 " --> pdb=" O LEU J2703 " (cutoff:3.500A) Processing helix chain 'J' and resid 2749 through 2774 removed outlier: 3.995A pdb=" N SER J2753 " --> pdb=" O GLU J2749 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE J2754 " --> pdb=" O LYS J2750 " (cutoff:3.500A) Processing helix chain 'J' and resid 2793 through 2798 removed outlier: 5.191A pdb=" N SER J2798 " --> pdb=" O TYR J2794 " (cutoff:3.500A) Processing helix chain 'J' and resid 2803 through 2820 Proline residue: J2808 - end of helix Processing helix chain 'J' and resid 2868 through 2895 Processing helix chain 'J' and resid 2907 through 2912 removed outlier: 4.879A pdb=" N THR J2912 " --> pdb=" O TYR J2908 " (cutoff:3.500A) Processing helix chain 'J' and resid 2917 through 2934 removed outlier: 3.622A pdb=" N ALA J2923 " --> pdb=" O ASP J2919 " (cutoff:3.500A) Processing helix chain 'J' and resid 2951 through 2979 Processing helix chain 'J' and resid 2991 through 3013 removed outlier: 3.569A pdb=" N LEU J3002 " --> pdb=" O PHE J2998 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU J3003 " --> pdb=" O ALA J2999 " (cutoff:3.500A) Proline residue: J3004 - end of helix removed outlier: 4.266A pdb=" N ASN J3007 " --> pdb=" O LEU J3003 " (cutoff:3.500A) Processing helix chain 'J' and resid 3033 through 3052 removed outlier: 4.280A pdb=" N HIS J3052 " --> pdb=" O ALA J3048 " (cutoff:3.500A) Processing helix chain 'J' and resid 3064 through 3073 removed outlier: 4.302A pdb=" N ARG J3073 " --> pdb=" O HIS J3069 " (cutoff:3.500A) Processing helix chain 'J' and resid 3089 through 3111 removed outlier: 4.103A pdb=" N ARG J3093 " --> pdb=" O LYS J3089 " (cutoff:3.500A) Processing helix chain 'J' and resid 3129 through 3150 removed outlier: 4.305A pdb=" N LEU J3137 " --> pdb=" O THR J3133 " (cutoff:3.500A) Proline residue: J3138 - end of helix Processing helix chain 'J' and resid 3160 through 3175 removed outlier: 3.875A pdb=" N SER J3164 " --> pdb=" O ASP J3160 " (cutoff:3.500A) Processing helix chain 'J' and resid 3187 through 3199 removed outlier: 4.684A pdb=" N GLY J3191 " --> pdb=" O ARG J3187 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA J3199 " --> pdb=" O ALA J3195 " (cutoff:3.500A) Processing helix chain 'J' and resid 3248 through 3257 removed outlier: 4.254A pdb=" N ALA J3257 " --> pdb=" O ILE J3253 " (cutoff:3.500A) Processing helix chain 'J' and resid 3267 through 3284 Proline residue: J3275 - end of helix Proline residue: J3282 - end of helix Processing helix chain 'J' and resid 3309 through 3326 Processing helix chain 'J' and resid 3337 through 3343 removed outlier: 4.062A pdb=" N GLN J3343 " --> pdb=" O ALA J3339 " (cutoff:3.500A) Processing helix chain 'J' and resid 3350 through 3379 removed outlier: 4.197A pdb=" N LEU J3354 " --> pdb=" O ARG J3350 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS J3355 " --> pdb=" O PRO J3351 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE J3359 " --> pdb=" O HIS J3355 " (cutoff:3.500A) Proline residue: J3360 - end of helix removed outlier: 3.758A pdb=" N LEU J3379 " --> pdb=" O GLU J3375 " (cutoff:3.500A) Processing helix chain 'J' and resid 3396 through 3421 removed outlier: 4.043A pdb=" N VAL J3400 " --> pdb=" O ASP J3396 " (cutoff:3.500A) Proline residue: J3410 - end of helix removed outlier: 3.654A pdb=" N TYR J3415 " --> pdb=" O LEU J3411 " (cutoff:3.500A) Processing helix chain 'J' and resid 3431 through 3448 Processing helix chain 'J' and resid 3449 through 3463 removed outlier: 3.671A pdb=" N GLN J3456 " --> pdb=" O LYS J3452 " (cutoff:3.500A) Processing helix chain 'J' and resid 3511 through 3524 removed outlier: 3.846A pdb=" N LYS J3516 " --> pdb=" O ALA J3512 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET J3517 " --> pdb=" O THR J3513 " (cutoff:3.500A) Proline residue: J3519 - end of helix removed outlier: 4.750A pdb=" N LEU J3522 " --> pdb=" O LEU J3518 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN J3523 " --> pdb=" O PRO J3519 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET J3524 " --> pdb=" O ILE J3520 " (cutoff:3.500A) Processing helix chain 'J' and resid 3529 through 3543 removed outlier: 6.724A pdb=" N ILE J3533 " --> pdb=" O ASP J3529 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N MET J3534 " --> pdb=" O GLN J3530 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS J3543 " --> pdb=" O ARG J3539 " (cutoff:3.500A) Processing helix chain 'J' and resid 3548 through 3553 Processing helix chain 'J' and resid 3588 through 3611 Processing helix chain 'J' and resid 3625 through 3638 removed outlier: 4.232A pdb=" N PHE J3636 " --> pdb=" O VAL J3632 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG J3637 " --> pdb=" O VAL J3633 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET J3638 " --> pdb=" O ALA J3634 " (cutoff:3.500A) Processing helix chain 'J' and resid 3640 through 3645 removed outlier: 3.952A pdb=" N LEU J3644 " --> pdb=" O PRO J3640 " (cutoff:3.500A) Proline residue: J3645 - end of helix No H-bonds generated for 'chain 'J' and resid 3640 through 3645' Processing helix chain 'J' and resid 3646 through 3665 removed outlier: 4.357A pdb=" N ILE J3662 " --> pdb=" O LYS J3658 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LEU J3663 " --> pdb=" O ALA J3659 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR J3664 " --> pdb=" O ALA J3660 " (cutoff:3.500A) Processing helix chain 'J' and resid 3669 through 3679 Processing helix chain 'J' and resid 3696 through 3711 Processing helix chain 'J' and resid 3719 through 3735 removed outlier: 3.890A pdb=" N ASP J3727 " --> pdb=" O MET J3723 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS J3734 " --> pdb=" O ALA J3730 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU J3735 " --> pdb=" O LYS J3731 " (cutoff:3.500A) Processing helix chain 'J' and resid 3752 through 3772 removed outlier: 4.049A pdb=" N LEU J3770 " --> pdb=" O GLN J3766 " (cutoff:3.500A) Processing helix chain 'J' and resid 3774 through 3787 removed outlier: 3.526A pdb=" N MET J3778 " --> pdb=" O GLY J3774 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS J3787 " --> pdb=" O ILE J3783 " (cutoff:3.500A) Processing helix chain 'J' and resid 3791 through 3806 Processing helix chain 'J' and resid 3809 through 3824 removed outlier: 3.611A pdb=" N GLN J3813 " --> pdb=" O ASN J3809 " (cutoff:3.500A) Processing helix chain 'J' and resid 3826 through 3840 removed outlier: 3.764A pdb=" N GLN J3830 " --> pdb=" O VAL J3826 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS J3839 " --> pdb=" O LEU J3835 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER J3840 " --> pdb=" O MET J3836 " (cutoff:3.500A) Processing helix chain 'J' and resid 3843 through 3857 removed outlier: 3.758A pdb=" N LEU J3856 " --> pdb=" O LYS J3852 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY J3857 " --> pdb=" O ALA J3853 " (cutoff:3.500A) Processing helix chain 'J' and resid 3866 through 3871 removed outlier: 7.061A pdb=" N ASN J3870 " --> pdb=" O ILE J3866 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY J3871 " --> pdb=" O ASN J3867 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 3866 through 3871' Processing helix chain 'J' and resid 3877 through 3893 removed outlier: 4.264A pdb=" N THR J3881 " --> pdb=" O ASP J3877 " (cutoff:3.500A) Processing helix chain 'J' and resid 3896 through 3906 removed outlier: 3.513A pdb=" N ARG J3904 " --> pdb=" O GLN J3900 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN J3906 " --> pdb=" O TYR J3902 " (cutoff:3.500A) Processing helix chain 'J' and resid 3914 through 3939 removed outlier: 3.524A pdb=" N CYS J3918 " --> pdb=" O ASN J3914 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY J3939 " --> pdb=" O TRP J3935 " (cutoff:3.500A) Processing helix chain 'J' and resid 3944 through 3970 Processing helix chain 'J' and resid 3973 through 3983 Processing helix chain 'J' and resid 3984 through 4007 removed outlier: 3.738A pdb=" N ASP J4006 " --> pdb=" O LYS J4002 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER J4007 " --> pdb=" O LEU J4003 " (cutoff:3.500A) Processing helix chain 'J' and resid 4009 through 4032 Processing helix chain 'J' and resid 4038 through 4052 Processing helix chain 'J' and resid 4053 through 4072 removed outlier: 4.573A pdb=" N LYS J4069 " --> pdb=" O PHE J4065 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP J4070 " --> pdb=" O LEU J4066 " (cutoff:3.500A) Processing helix chain 'J' and resid 4074 through 4081 removed outlier: 3.817A pdb=" N TYR J4080 " --> pdb=" O ALA J4076 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL J4081 " --> pdb=" O PHE J4077 " (cutoff:3.500A) Processing helix chain 'J' and resid 4089 through 4101 Processing helix chain 'J' and resid 4104 through 4115 Processing helix chain 'J' and resid 4124 through 4137 removed outlier: 4.344A pdb=" N PHE J4132 " --> pdb=" O PHE J4128 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN J4133 " --> pdb=" O ALA J4129 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU J4134 " --> pdb=" O ASN J4130 " (cutoff:3.500A) Proline residue: J4135 - end of helix Processing helix chain 'J' and resid 4138 through 4154 Processing helix chain 'J' and resid 4157 through 4168 removed outlier: 3.919A pdb=" N ASN J4162 " --> pdb=" O PRO J4158 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE J4163 " --> pdb=" O ARG J4159 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU J4168 " --> pdb=" O LEU J4164 " (cutoff:3.500A) Processing helix chain 'J' and resid 4169 through 4179 Proline residue: J4176 - end of helix removed outlier: 4.931A pdb=" N GLY J4179 " --> pdb=" O ARG J4175 " (cutoff:3.500A) Processing helix chain 'J' and resid 4198 through 4208 removed outlier: 3.667A pdb=" N MET J4207 " --> pdb=" O ALA J4203 " (cutoff:3.500A) Proline residue: J4208 - end of helix Processing helix chain 'J' and resid 4209 through 4225 removed outlier: 3.656A pdb=" N SER J4213 " --> pdb=" O GLN J4209 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL J4222 " --> pdb=" O ILE J4218 " (cutoff:3.500A) Processing helix chain 'J' and resid 4227 through 4252 removed outlier: 4.439A pdb=" N MET J4231 " --> pdb=" O GLU J4227 " (cutoff:3.500A) Processing helix chain 'J' and resid 4323 through 4341 removed outlier: 3.809A pdb=" N ALA J4327 " --> pdb=" O THR J4323 " (cutoff:3.500A) Processing helix chain 'J' and resid 4541 through 4559 removed outlier: 3.973A pdb=" N GLU J4545 " --> pdb=" O TRP J4541 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN J4558 " --> pdb=" O TYR J4554 " (cutoff:3.500A) Processing helix chain 'J' and resid 4560 through 4580 removed outlier: 4.054A pdb=" N PHE J4579 " --> pdb=" O PHE J4575 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR J4580 " --> pdb=" O ILE J4576 " (cutoff:3.500A) Processing helix chain 'J' and resid 4635 through 4684 removed outlier: 3.867A pdb=" N MET J4639 " --> pdb=" O SER J4635 " (cutoff:3.500A) Proline residue: J4641 - end of helix removed outlier: 3.581A pdb=" N TRP J4644 " --> pdb=" O GLU J4640 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU J4648 " --> pdb=" O TRP J4644 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL J4666 " --> pdb=" O ASN J4662 " (cutoff:3.500A) Proline residue: J4667 - end of helix Processing helix chain 'J' and resid 4685 through 4690 Processing helix chain 'J' and resid 4696 through 4709 removed outlier: 4.128A pdb=" N ARG J4703 " --> pdb=" O GLY J4699 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU J4704 " --> pdb=" O GLN J4700 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL J4705 " --> pdb=" O TRP J4701 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU J4706 " --> pdb=" O ASP J4702 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN J4707 " --> pdb=" O ARG J4703 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR J4708 " --> pdb=" O LEU J4704 " (cutoff:3.500A) Proline residue: J4709 - end of helix Processing helix chain 'J' and resid 4719 through 4733 removed outlier: 5.342A pdb=" N ASP J4730 " --> pdb=" O ASP J4726 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE J4731 " --> pdb=" O LYS J4727 " (cutoff:3.500A) Processing helix chain 'J' and resid 4734 through 4742 removed outlier: 3.848A pdb=" N GLU J4739 " --> pdb=" O GLU J4735 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU J4740 " --> pdb=" O ARG J4736 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY J4742 " --> pdb=" O ALA J4738 " (cutoff:3.500A) Processing helix chain 'J' and resid 4745 through 4755 removed outlier: 3.811A pdb=" N GLU J4749 " --> pdb=" O LEU J4745 " (cutoff:3.500A) Processing helix chain 'J' and resid 4766 through 4771 removed outlier: 3.570A pdb=" N SER J4770 " --> pdb=" O THR J4766 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE J4771 " --> pdb=" O TRP J4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4766 through 4771' Processing helix chain 'J' and resid 4772 through 4786 Processing helix chain 'J' and resid 4787 through 4805 removed outlier: 4.343A pdb=" N HIS J4803 " --> pdb=" O SER J4799 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR J4804 " --> pdb=" O LEU J4800 " (cutoff:3.500A) Processing helix chain 'J' and resid 4808 through 4820 removed outlier: 4.529A pdb=" N HIS J4812 " --> pdb=" O PHE J4808 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU J4813 " --> pdb=" O PHE J4809 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU J4814 " --> pdb=" O ALA J4810 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP J4815 " --> pdb=" O ALA J4811 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ILE J4816 " --> pdb=" O HIS J4812 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA J4817 " --> pdb=" O LEU J4813 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL J4820 " --> pdb=" O ILE J4816 " (cutoff:3.500A) Processing helix chain 'J' and resid 4821 through 4833 removed outlier: 3.772A pdb=" N VAL J4830 " --> pdb=" O ILE J4826 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR J4831 " --> pdb=" O LEU J4827 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN J4833 " --> pdb=" O SER J4829 " (cutoff:3.500A) Processing helix chain 'J' and resid 4834 through 4859 Processing helix chain 'J' and resid 4878 through 4889 Processing helix chain 'J' and resid 4897 through 4902 removed outlier: 5.326A pdb=" N GLU J4902 " --> pdb=" O GLY J4898 " (cutoff:3.500A) Processing helix chain 'J' and resid 4909 through 4924 removed outlier: 3.610A pdb=" N PHE J4916 " --> pdb=" O TYR J4912 " (cutoff:3.500A) Processing helix chain 'J' and resid 4928 through 4953 removed outlier: 3.595A pdb=" N LYS J4951 " --> pdb=" O GLN J4947 " (cutoff:3.500A) Processing helix chain 'J' and resid 4965 through 4972 removed outlier: 3.683A pdb=" N THR J4970 " --> pdb=" O ASP J4966 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR J4971 " --> pdb=" O TYR J4967 " (cutoff:3.500A) Proline residue: J4972 - end of helix Processing helix chain 'J' and resid 4973 through 4981 removed outlier: 3.842A pdb=" N THR J4977 " --> pdb=" O HIS J4973 " (cutoff:3.500A) Processing helix chain 'J' and resid 4984 through 4999 removed outlier: 3.940A pdb=" N TYR J4988 " --> pdb=" O ASN J4984 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET J4989 " --> pdb=" O LEU J4985 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE J4990 " --> pdb=" O ALA J4986 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASP J4999 " --> pdb=" O LEU J4995 " (cutoff:3.500A) Processing helix chain 'J' and resid 5004 through 5017 Processing helix chain 'J' and resid 5027 through 5033 Processing helix chain 'J' and resid 54 through 59 Proline residue: J 59 - end of helix No H-bonds generated for 'chain 'J' and resid 54 through 59' Processing helix chain 'L' and resid 6 through 21 removed outlier: 3.966A pdb=" N SER L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU L 19 " --> pdb=" O GLU L 15 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 41 removed outlier: 3.557A pdb=" N GLY L 34 " --> pdb=" O THR L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 56 removed outlier: 3.525A pdb=" N VAL L 56 " --> pdb=" O MET L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 93 removed outlier: 3.727A pdb=" N ASP L 79 " --> pdb=" O ARG L 75 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU L 83 " --> pdb=" O ASP L 79 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU L 84 " --> pdb=" O THR L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 112 removed outlier: 3.561A pdb=" N ALA L 105 " --> pdb=" O ILE L 101 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU L 106 " --> pdb=" O SER L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 128 Processing helix chain 'L' and resid 138 through 148 Processing sheet with id= 1, first strand: chain 'D' and resid 47 through 52 removed outlier: 4.254A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 12.840A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.669A pdb=" N ILE D 170 " --> pdb=" O HIS D 151 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 220 through 224 Processing sheet with id= 4, first strand: chain 'D' and resid 229 through 233 Processing sheet with id= 5, first strand: chain 'D' and resid 290 through 293 Processing sheet with id= 6, first strand: chain 'D' and resid 315 through 318 Processing sheet with id= 7, first strand: chain 'D' and resid 634 through 639 No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'D' and resid 682 through 686 removed outlier: 3.593A pdb=" N ARG D 683 " --> pdb=" O SER D 782 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 754 through 758 removed outlier: 3.725A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 742 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 664 " --> pdb=" O CYS D 746 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 748 " --> pdb=" O TRP D 662 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU D 665 " --> pdb=" O LEU D 792 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 667 " --> pdb=" O ARG D 790 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 766 through 769 Processing sheet with id= 11, first strand: chain 'D' and resid 829 through 832 removed outlier: 4.676A pdb=" N TYR D 829 " --> pdb=" O VAL D 840 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLY D1086 " --> pdb=" O LEU D1155 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET D1152 " --> pdb=" O ILE D1161 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 1134 through 1138 removed outlier: 3.710A pdb=" N VAL D1123 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D1102 " --> pdb=" O PHE D1124 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY D1126 " --> pdb=" O MET D1100 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D1073 " --> pdb=" O LEU D1194 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N VAL D1072 " --> pdb=" O SER D1241 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER D1241 " --> pdb=" O VAL D1072 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR D1236 " --> pdb=" O MET D1608 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 1243 through 1247 removed outlier: 3.812A pdb=" N GLN D1244 " --> pdb=" O MET D1601 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET D1601 " --> pdb=" O GLN D1244 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU D1596 " --> pdb=" O SER D1292 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D1600 " --> pdb=" O PHE D1288 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) removed outlier: 13.145A pdb=" N MET D1286 " --> pdb=" O PRO D1602 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU D1287 " --> pdb=" O VAL D1554 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D1554 " --> pdb=" O LEU D1287 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D1552 " --> pdb=" O LEU D1289 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 1255 through 1263 removed outlier: 6.495A pdb=" N VAL D1561 " --> pdb=" O PHE D1440 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY D1567 " --> pdb=" O TYR D1434 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR D1434 " --> pdb=" O GLY D1567 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR D1431 " --> pdb=" O LEU D1522 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D1435 " --> pdb=" O CYS D1518 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D1514 " --> pdb=" O VAL D1439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D1521 " --> pdb=" O LEU D1526 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU D1526 " --> pdb=" O ASP D1521 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY D1525 " --> pdb=" O VAL D1542 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE D1540 " --> pdb=" O MET D1527 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 5.189A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D4179 " --> pdb=" O PHE D4195 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE D4195 " --> pdb=" O GLY D4179 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 4581 through 4584 Processing sheet with id= 17, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.792A pdb=" N GLU E 5 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 45 through 49 removed outlier: 7.467A pdb=" N VAL E 23 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU E 102 " --> pdb=" O HIS E 25 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.557A pdb=" N GLU B 5 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG B 71 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 45 through 49 removed outlier: 3.655A pdb=" N VAL B 24 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL B 23 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 25 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 102 " --> pdb=" O HIS B 25 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 4 through 7 removed outlier: 6.815A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 45 through 49 removed outlier: 7.403A pdb=" N VAL H 23 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP H 100 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 4 through 7 removed outlier: 6.415A pdb=" N ARG K 71 " --> pdb=" O ILE K 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 45 through 49 removed outlier: 3.884A pdb=" N PHE K 48 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL K 23 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS K 25 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU K 102 " --> pdb=" O HIS K 25 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'A' and resid 22 through 28 removed outlier: 4.872A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.750A pdb=" N LEU A 108 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'A' and resid 148 through 152 Processing sheet with id= 28, first strand: chain 'A' and resid 181 through 184 Processing sheet with id= 29, first strand: chain 'A' and resid 217 through 221 removed outlier: 4.388A pdb=" N HIS A 218 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 262 " --> pdb=" O HIS A 218 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'A' and resid 245 through 248 removed outlier: 6.025A pdb=" N VAL A 245 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LYS A 374 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS A 375 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= 32, first strand: chain 'A' and resid 635 through 640 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'A' and resid 682 through 686 Processing sheet with id= 34, first strand: chain 'A' and resid 754 through 758 removed outlier: 3.587A pdb=" N SER A 754 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP A 749 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP A 742 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 664 " --> pdb=" O CYS A 746 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 787 " --> pdb=" O CYS A1630 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'A' and resid 765 through 769 Processing sheet with id= 36, first strand: chain 'A' and resid 829 through 832 removed outlier: 4.433A pdb=" N TYR A 829 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY A1086 " --> pdb=" O LEU A1155 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'A' and resid 1005 through 1008 Processing sheet with id= 38, first strand: chain 'A' and resid 1134 through 1137 removed outlier: 3.629A pdb=" N VAL A1102 " --> pdb=" O PHE A1124 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A1194 " --> pdb=" O ARG A1073 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A1073 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N VAL A1072 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N SER A1241 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1239 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR A1236 " --> pdb=" O MET A1608 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A1604 " --> pdb=" O LYS A1240 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 3.740A pdb=" N GLN A1244 " --> pdb=" O MET A1601 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A1601 " --> pdb=" O GLN A1244 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A1287 " --> pdb=" O VAL A1554 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A1554 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A1552 " --> pdb=" O LEU A1289 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'A' and resid 1267 through 1271 removed outlier: 6.453A pdb=" N VAL A1561 " --> pdb=" O PHE A1440 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE A1440 " --> pdb=" O VAL A1561 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLY A1567 " --> pdb=" O TYR A1434 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR A1434 " --> pdb=" O GLY A1567 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A1435 " --> pdb=" O CYS A1518 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A1514 " --> pdb=" O VAL A1439 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'A' and resid 2780 through 2783 removed outlier: 6.467A pdb=" N VAL A2781 " --> pdb=" O HIS A2788 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS A2788 " --> pdb=" O VAL A2781 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLU A2783 " --> pdb=" O LYS A2786 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'A' and resid 2821 through 2825 Processing sheet with id= 43, first strand: chain 'A' and resid 4177 through 4184 removed outlier: 5.064A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A4179 " --> pdb=" O PHE A4195 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A4195 " --> pdb=" O GLY A4179 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A4181 " --> pdb=" O ILE A4193 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A4193 " --> pdb=" O ILE A4181 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 22 through 28 removed outlier: 5.218A pdb=" N LEU G 22 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS G 34 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 109 through 112 removed outlier: 5.445A pdb=" N LEU G 109 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET G 116 " --> pdb=" O HIS G 111 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'G' and resid 148 through 152 Processing sheet with id= 47, first strand: chain 'G' and resid 180 through 184 Processing sheet with id= 48, first strand: chain 'G' and resid 229 through 233 Processing sheet with id= 49, first strand: chain 'G' and resid 280 through 284 removed outlier: 4.635A pdb=" N HIS G 218 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'G' and resid 290 through 293 Processing sheet with id= 51, first strand: chain 'G' and resid 314 through 318 Processing sheet with id= 52, first strand: chain 'G' and resid 636 through 640 No H-bonds generated for sheet with id= 52 Processing sheet with id= 53, first strand: chain 'G' and resid 682 through 686 removed outlier: 3.560A pdb=" N ARG G 683 " --> pdb=" O SER G 782 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'G' and resid 754 through 758 removed outlier: 4.059A pdb=" N TRP G 662 " --> pdb=" O LEU G 748 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU G 665 " --> pdb=" O LEU G 792 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU G 792 " --> pdb=" O GLU G 665 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS G 788 " --> pdb=" O ASP G 669 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'G' and resid 766 through 769 removed outlier: 3.518A pdb=" N VAL G 767 " --> pdb=" O THR G1475 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER G1485 " --> pdb=" O MET G1476 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'G' and resid 829 through 833 removed outlier: 4.578A pdb=" N TYR G 829 " --> pdb=" O VAL G 840 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY G 836 " --> pdb=" O GLY G 833 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU G1202 " --> pdb=" O PRO G 837 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN G1198 " --> pdb=" O GLY G 841 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL G1199 " --> pdb=" O VAL G1095 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE G1090 " --> pdb=" O CYS G1151 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G1159 " --> pdb=" O ASP G1154 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'G' and resid 1122 through 1126 removed outlier: 3.519A pdb=" N VAL G1102 " --> pdb=" O PHE G1124 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET G1100 " --> pdb=" O GLY G1126 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU G1099 " --> pdb=" O GLY G1195 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU G1194 " --> pdb=" O ARG G1073 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG G1073 " --> pdb=" O LEU G1194 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N VAL G1072 " --> pdb=" O SER G1241 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER G1241 " --> pdb=" O VAL G1072 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE G1074 " --> pdb=" O SER G1239 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR G1235 " --> pdb=" O GLU G1078 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER G1604 " --> pdb=" O LYS G1240 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 1243 through 1247 removed outlier: 3.903A pdb=" N LEU G1287 " --> pdb=" O VAL G1554 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL G1554 " --> pdb=" O LEU G1287 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G1552 " --> pdb=" O LEU G1289 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'G' and resid 1267 through 1272 removed outlier: 4.102A pdb=" N ILE G1562 " --> pdb=" O LEU G1272 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL G1561 " --> pdb=" O PHE G1440 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLY G1567 " --> pdb=" O TYR G1434 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TYR G1434 " --> pdb=" O GLY G1567 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N THR G1431 " --> pdb=" O LEU G1522 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR G1435 " --> pdb=" O CYS G1518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G1526 " --> pdb=" O ASP G1521 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLY G1525 " --> pdb=" O VAL G1542 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'G' and resid 2780 through 2783 removed outlier: 6.467A pdb=" N VAL G2781 " --> pdb=" O HIS G2788 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS G2788 " --> pdb=" O VAL G2781 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLU G2783 " --> pdb=" O LYS G2786 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'G' and resid 2821 through 2825 Processing sheet with id= 62, first strand: chain 'G' and resid 4177 through 4182 removed outlier: 5.158A pdb=" N TYR G4177 " --> pdb=" O ILE G4197 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY G4179 " --> pdb=" O PHE G4195 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G4195 " --> pdb=" O GLY G4179 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 47 through 51 removed outlier: 3.565A pdb=" N CYS J 36 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL J 21 " --> pdb=" O ASN J 203 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN J 203 " --> pdb=" O VAL J 21 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 149 through 153 removed outlier: 3.972A pdb=" N ALA J 153 " --> pdb=" O ASP J 168 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP J 168 " --> pdb=" O ALA J 153 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'J' and resid 230 through 233 Processing sheet with id= 66, first strand: chain 'J' and resid 288 through 291 removed outlier: 3.574A pdb=" N ARG J 289 " --> pdb=" O HIS J 284 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU J 291 " --> pdb=" O ILE J 282 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE J 282 " --> pdb=" O LEU J 291 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL J 285 " --> pdb=" O LEU J 259 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N LEU J 259 " --> pdb=" O VAL J 285 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU J 262 " --> pdb=" O HIS J 218 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N HIS J 218 " --> pdb=" O LEU J 262 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG J 221 " --> pdb=" O THR J 391 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR J 391 " --> pdb=" O ARG J 221 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE J 223 " --> pdb=" O PHE J 389 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'J' and resid 315 through 318 Processing sheet with id= 68, first strand: chain 'J' and resid 636 through 639 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'J' and resid 681 through 686 removed outlier: 5.035A pdb=" N HIS J 681 " --> pdb=" O SER J 784 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER J 784 " --> pdb=" O HIS J 681 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG J 683 " --> pdb=" O SER J 782 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'J' and resid 714 through 717 removed outlier: 3.690A pdb=" N GLY J 715 " --> pdb=" O TRP J 722 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS J 720 " --> pdb=" O ASP J 717 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'J' and resid 753 through 759 removed outlier: 3.992A pdb=" N SER J 754 " --> pdb=" O ASP J 749 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP J 749 " --> pdb=" O SER J 754 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER J 756 " --> pdb=" O CYS J 747 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG J 758 " --> pdb=" O SER J 745 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLY J 660 " --> pdb=" O LEU J 750 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU J 665 " --> pdb=" O LEU J 792 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS J 788 " --> pdb=" O ASP J 669 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLY J1625 " --> pdb=" O ALA J1620 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'J' and resid 765 through 769 removed outlier: 4.709A pdb=" N GLN J 765 " --> pdb=" O GLY J1477 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY J1477 " --> pdb=" O GLN J 765 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER J1485 " --> pdb=" O MET J1476 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'J' and resid 829 through 833 removed outlier: 4.617A pdb=" N TYR J 829 " --> pdb=" O VAL J 840 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY J 833 " --> pdb=" O GLY J 836 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU J1202 " --> pdb=" O PRO J 837 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN J1198 " --> pdb=" O GLY J 841 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'J' and resid 1005 through 1008 Processing sheet with id= 75, first strand: chain 'J' and resid 1134 through 1137 removed outlier: 3.544A pdb=" N VAL J1102 " --> pdb=" O PHE J1124 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY J1126 " --> pdb=" O MET J1100 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N MET J1100 " --> pdb=" O GLY J1126 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU J1099 " --> pdb=" O GLY J1195 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG J1101 " --> pdb=" O SER J1193 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU J1194 " --> pdb=" O ARG J1073 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N VAL J1072 " --> pdb=" O SER J1241 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER J1241 " --> pdb=" O VAL J1072 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE J1074 " --> pdb=" O SER J1239 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR J1235 " --> pdb=" O GLU J1078 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'J' and resid 1149 through 1155 Processing sheet with id= 77, first strand: chain 'J' and resid 1267 through 1271 removed outlier: 6.411A pdb=" N VAL J1561 " --> pdb=" O PHE J1440 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE J1440 " --> pdb=" O VAL J1561 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY J1567 " --> pdb=" O TYR J1434 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR J1434 " --> pdb=" O GLY J1567 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR J1431 " --> pdb=" O LEU J1522 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J1514 " --> pdb=" O VAL J1439 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP J1521 " --> pdb=" O LEU J1526 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU J1526 " --> pdb=" O ASP J1521 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY J1525 " --> pdb=" O VAL J1542 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'J' and resid 1550 through 1555 removed outlier: 3.659A pdb=" N VAL J1552 " --> pdb=" O LEU J1289 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU J1287 " --> pdb=" O VAL J1554 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE J1288 " --> pdb=" O LEU J1600 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU J1596 " --> pdb=" O SER J1292 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'J' and resid 2780 through 2783 removed outlier: 6.468A pdb=" N VAL J2781 " --> pdb=" O HIS J2788 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS J2788 " --> pdb=" O VAL J2781 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLU J2783 " --> pdb=" O LYS J2786 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'J' and resid 2821 through 2825 Processing sheet with id= 81, first strand: chain 'J' and resid 4180 through 4184 removed outlier: 3.769A pdb=" N ILE J4183 " --> pdb=" O GLU J4191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU J4191 " --> pdb=" O ILE J4183 " (cutoff:3.500A) 7030 hydrogen bonds defined for protein. 21012 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: 77.86 Time building geometry restraints manager: 38.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 36078 1.34 - 1.46: 28140 1.46 - 1.59: 51345 1.59 - 1.71: 16 1.71 - 1.84: 992 Bond restraints: 116571 Sorted by residual: bond pdb=" C ARG G3762 " pdb=" O ARG G3762 " ideal model delta sigma weight residual 1.236 1.307 -0.070 1.15e-02 7.56e+03 3.72e+01 bond pdb=" C GLN G3766 " pdb=" O GLN G3766 " ideal model delta sigma weight residual 1.237 1.302 -0.066 1.17e-02 7.31e+03 3.15e+01 bond pdb=" N VAL J2495 " pdb=" CA VAL J2495 " ideal model delta sigma weight residual 1.460 1.491 -0.030 7.30e-03 1.88e+04 1.72e+01 bond pdb=" N LEU G3770 " pdb=" CA LEU G3770 " ideal model delta sigma weight residual 1.458 1.508 -0.050 1.28e-02 6.10e+03 1.53e+01 bond pdb=" N GLN G3766 " pdb=" CA GLN G3766 " ideal model delta sigma weight residual 1.459 1.498 -0.038 1.21e-02 6.83e+03 1.01e+01 ... (remaining 116566 not shown) Histogram of bond angle deviations from ideal: 96.75 - 105.37: 2542 105.37 - 114.00: 67235 114.00 - 122.63: 79078 122.63 - 131.26: 10414 131.26 - 139.89: 274 Bond angle restraints: 159543 Sorted by residual: angle pdb=" N GLU A 338 " pdb=" CA GLU A 338 " pdb=" C GLU A 338 " ideal model delta sigma weight residual 108.79 122.33 -13.54 1.53e+00 4.27e-01 7.84e+01 angle pdb=" C ALA J1675 " pdb=" CA ALA J1675 " pdb=" CB ALA J1675 " ideal model delta sigma weight residual 116.54 109.79 6.75 1.15e+00 7.56e-01 3.44e+01 angle pdb=" C GLU D 338 " pdb=" CA GLU D 338 " pdb=" CB GLU D 338 " ideal model delta sigma weight residual 116.63 109.88 6.75 1.16e+00 7.43e-01 3.39e+01 angle pdb=" N GLY G2934 " pdb=" CA GLY G2934 " pdb=" C GLY G2934 " ideal model delta sigma weight residual 115.32 107.40 7.92 1.38e+00 5.25e-01 3.29e+01 angle pdb=" N GLY J2934 " pdb=" CA GLY J2934 " pdb=" C GLY J2934 " ideal model delta sigma weight residual 115.32 107.41 7.91 1.38e+00 5.25e-01 3.29e+01 ... (remaining 159538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 63555 17.83 - 35.66: 3744 35.66 - 53.50: 612 53.50 - 71.33: 73 71.33 - 89.16: 61 Dihedral angle restraints: 68045 sinusoidal: 19560 harmonic: 48485 Sorted by residual: dihedral pdb=" CA GLY J2525 " pdb=" C GLY J2525 " pdb=" N PHE J2526 " pdb=" CA PHE J2526 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ASN G3950 " pdb=" C ASN G3950 " pdb=" N PHE G3951 " pdb=" CA PHE G3951 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA GLY A2525 " pdb=" C GLY A2525 " pdb=" N PHE A2526 " pdb=" CA PHE A2526 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 68042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 17347 0.068 - 0.136: 1673 0.136 - 0.204: 120 0.204 - 0.272: 8 0.272 - 0.340: 1 Chirality restraints: 19149 Sorted by residual: chirality pdb=" CB ILE A4218 " pdb=" CA ILE A4218 " pdb=" CG1 ILE A4218 " pdb=" CG2 ILE A4218 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CG LEU D 600 " pdb=" CB LEU D 600 " pdb=" CD1 LEU D 600 " pdb=" CD2 LEU D 600 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CG LEU A 600 " pdb=" CB LEU A 600 " pdb=" CD1 LEU A 600 " pdb=" CD2 LEU A 600 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 19146 not shown) Planarity restraints: 20607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D1143 " -0.024 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP D1143 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP D1143 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D1143 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D1143 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D1143 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D1143 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1143 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1143 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D1143 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J2527 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO J2528 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO J2528 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO J2528 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN D4020 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" CD GLN D4020 " -0.048 2.00e-02 2.50e+03 pdb=" OE1 GLN D4020 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN D4020 " 0.016 2.00e-02 2.50e+03 ... (remaining 20604 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 6192 2.74 - 3.28: 120684 3.28 - 3.82: 194237 3.82 - 4.36: 199271 4.36 - 4.90: 349898 Nonbonded interactions: 870282 Sorted by model distance: nonbonded pdb=" O LEU J3842 " pdb=" OG SER J3929 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR A4687 " pdb=" O GLY A4699 " model vdw 2.198 2.440 nonbonded pdb=" O ILE G1426 " pdb=" OG1 THR G1430 " model vdw 2.202 2.440 nonbonded pdb=" O GLY J 417 " pdb=" OG SER J 420 " model vdw 2.209 2.440 nonbonded pdb=" O LEU G3842 " pdb=" OG SER G3929 " model vdw 2.210 2.440 ... (remaining 870277 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 11 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 156 or (resid 157 through 159 and \ (name N or name CA or name C or name O or name CB )) or (resid 160 through 162 a \ nd (name N or name CA or name C or name O or name CB )) or resid 163 through 183 \ or (resid 184 through 186 and (name N or name CA or name C or name O or name CB \ )) or (resid 187 through 189 and (name N or name CA or name C or name O or name \ CB )) or resid 190 through 196 or (resid 197 through 198 and (name N or name CA \ or name C or name O or name CB )) or resid 199 through 219 or (resid 220 throug \ h 221 and (name N or name CA or name C or name O or name CB )) or resid 222 thro \ ugh 230 or (resid 231 through 244 and (name N or name CA or name C or name O or \ name CB )) or resid 245 through 256 or (resid 257 and (name N or name CA or name \ C or name O or name CB )) or resid 258 through 266 or (resid 267 through 268 an \ d (name N or name CA or name C or name O or name CB )) or resid 269 through 273 \ or (resid 274 and (name N or name CA or name C or name O or name CB )) or resid \ 275 through 290 or (resid 291 through 297 and (name N or name CA or name C or na \ me O or name CB )) or resid 298 or (resid 299 and (name N or name CA or name C o \ r name O or name CB )) or resid 300 through 301 or (resid 302 through 307 and (n \ ame N or name CA or name C or name O or name CB )) or resid 308 through 314 or ( \ resid 315 and (name N or name CA or name C or name O or name CB )) or resid 316 \ through 333 or (resid 334 and (name N or name CA or name C or name O or name CB \ )) or resid 335 through 348 or (resid 349 and (name N or name CA or name C or na \ me O or name CB )) or resid 350 through 373 or (resid 374 and (name N or name CA \ or name C or name O or name CB )) or resid 375 through 393 or (resid 394 and (n \ ame N or name CA or name C or name O or name CB )) or resid 395 through 401 or ( \ resid 402 and (name N or name CA or name C or name O or name CB )) or resid 403 \ through 417 or (resid 418 and (name N or name CA or name C or name O or name CB \ )) or resid 419 through 471 or (resid 472 and (name N or name CA or name C or na \ me O or name CB )) or resid 473 through 532 or (resid 533 through 535 and (name \ N or name CA or name C or name O or name CB )) or resid 536 through 549 or (resi \ d 550 and (name N or name CA or name C or name O or name CB )) or resid 551 thro \ ugh 583 or (resid 584 and (name N or name CA or name C or name O or name CB )) o \ r resid 585 through 718 or (resid 719 and (name N or name CA or name C or name O \ or name CB )) or resid 720 or (resid 721 and (name N or name CA or name C or na \ me O or name CB )) or resid 722 through 734 or (resid 735 and (name N or name CA \ or name C or name O or name CB )) or resid 736 through 746 or (resid 747 throug \ h 749 and (name N or name CA or name C or name O or name CB )) or resid 750 thro \ ugh 751 or (resid 752 and (name N or name CA or name C or name O or name CB )) o \ r resid 753 through 757 or (resid 758 and (name N or name CA or name C or name O \ or name CB )) or resid 759 through 772 or (resid 773 through 774 and (name N or \ name CA or name C or name O or name CB )) or resid 775 or (resid 776 and (name \ N or name CA or name C or name O or name CB )) or resid 777 through 791 or (resi \ d 792 through 793 and (name N or name CA or name C or name O or name CB )) or (r \ esid 794 through 797 and (name N or name CA or name C or name O or name CB )) or \ resid 798 through 815 or (resid 816 and (name N or name CA or name C or name O \ or name CB )) or resid 817 through 830 or (resid 831 through 832 and (name N or \ name CA or name C or name O or name CB )) or resid 833 through 1023 or (resid 10 \ 24 through 1047 and (name N or name CA or name C or name O or name CB )) or resi \ d 1048 through 1086 or (resid 1087 and (name N or name CA or name C or name O or \ name CB )) or resid 1088 through 1092 or (resid 1093 through 1094 and (name N o \ r name CA or name C or name O or name CB )) or resid 1095 through 1100 or (resid \ 1101 and (name N or name CA or name C or name O or name CB )) or resid 1102 thr \ ough 1138 or (resid 1139 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1140 or (resid 1141 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1142 or (resid 1143 through 1144 and (name N or name CA or name \ C or name O or name CB )) or resid 1145 through 1150 or (resid 1151 and (name N \ or name CA or name C or name O or name CB )) or resid 1152 through 1159 or (res \ id 1160 and (name N or name CA or name C or name O or name CB )) or resid 1161 t \ hrough 1169 or (resid 1170 and (name N or name CA or name C or name O or name CB \ )) or resid 1171 through 1179 or (resid 1180 through 1183 and (name N or name C \ A or name C or name O or name CB )) or resid 1184 through 1205 or (resid 1206 th \ rough 1212 and (name N or name CA or name C or name O or name CB )) or resid 121 \ 3 through 1227 or (resid 1228 and (name N or name CA or name C or name O or name \ CB )) or resid 1229 or (resid 1230 through 1231 and (name N or name CA or name \ C or name O or name CB )) or resid 1232 through 1239 or (resid 1240 and (name N \ or name CA or name C or name O or name CB )) or resid 1241 through 1259 or (resi \ d 1260 through 1261 and (name N or name CA or name C or name O or name CB )) or \ resid 1262 through 1274 or (resid 1275 through 1276 and (name N or name CA or na \ me C or name O or name CB )) or resid 1277 through 1283 or (resid 1284 through 1 \ 285 and (name N or name CA or name C or name O or name CB )) or resid 1286 throu \ gh 1298 or (resid 1299 through 1423 and (name N or name CA or name C or name O o \ r name CB )) or resid 1424 through 1426 or (resid 1427 and (name N or name CA or \ name C or name O or name CB )) or resid 1428 through 1461 or 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CA or name C or name O or name CB )) or (resid 4185 through 4191 and ( \ name N or name CA or name C or name O or name CB )) or resid 4192 through 4229 o \ r (resid 4230 through 4231 and (name N or name CA or name C or name O or name CB \ )) or resid 4232 through 4253 or (resid 4323 through 4328 and (name N or name C \ A or name C or name O or name CB )) or resid 4329 through 4673 or (resid 4674 th \ rough 4676 and (name N or name CA or name C or name O or name CB )) or resid 467 \ 7 through 4679 or (resid 4680 and (name N or name CA or name C or name O or name \ CB )) or resid 4681 through 4717 or (resid 4718 and (name N or name CA or name \ C or name O or name CB )) or resid 4719 through 4726 or (resid 4727 and (name N \ or name CA or name C or name O or name CB )) or resid 4728 through 4742 or (resi \ d 4743 through 4746 and (name N or name CA or name C or name O or name CB )) or \ resid 4747 through 4755 or (resid 4766 through 4771 and (name N or name CA or na \ me C or name O or 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name CA or name C or name O or name C \ B )) or resid 1645 through 1648 or (resid 1649 and (name N or name CA or name C \ or name O or name CB )) or resid 1650 through 1686 or (resid 1687 and (name N or \ name CA or name C or name O or name CB )) or resid 1688 through 1801 or (resid \ 1802 and (name N or name CA or name C or name O or name CB )) or resid 1803 thro \ ugh 1809 or (resid 1810 through 1811 and (name N or name CA or name C or name O \ or name CB )) or resid 1812 through 1859 or (resid 1860 and (name N or name CA o \ r name C or name O or name CB )) or resid 1861 through 1928 or (resid 1929 throu \ gh 1930 and (name N or name CA or name C or name O or name CB )) or resid 1931 t \ hrough 1995 or (resid 1996 through 2000 and (name N or name CA or name C or name \ O or name CB )) or resid 2001 through 2002 or (resid 2003 through 2004 and (nam \ e N or name CA or name C or name O or name CB )) or resid 2005 through 2020 or ( \ resid 2021 and (name N or name CA or name C or name 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throug \ h 532 or (resid 533 through 535 and (name N or name CA or name C or name O or na \ me CB )) or resid 536 through 549 or (resid 550 and (name N or name CA or name C \ or name O or name CB )) or resid 551 through 583 or (resid 584 and (name N or n \ ame CA or name C or name O or name CB )) or resid 585 through 625 or (resid 626 \ and (name N or name CA or name C or name O or name CB )) or resid 627 through 64 \ 6 or (resid 647 and (name N or name CA or name C or name O or name CB )) or resi \ d 648 through 718 or (resid 719 and (name N or name CA or name C or name O or na \ me CB )) or resid 720 or (resid 721 and (name N or name CA or name C or name O o \ r name CB )) or resid 722 through 734 or (resid 735 and (name N or name CA or na \ me C or name O or name CB )) or resid 736 through 745 or (resid 746 through 749 \ and (name N or name CA or name C or name O or name CB )) or resid 750 through 75 \ 1 or (resid 752 and (name N or name CA or name C or name O or name CB )) or resi \ d 753 through 757 or (resid 758 and (name N or name CA or name C or name O or na \ me CB )) or resid 759 through 772 or (resid 773 through 774 and (name N or name \ CA or name C or name O or name CB )) or resid 775 or (resid 776 and (name N or n \ ame CA or name C or name O or name CB )) or resid 777 through 791 or (resid 792 \ through 793 and (name N or name CA or name C or name O or name CB )) or (resid 7 \ 94 through 797 and (name N or name CA or name C or name O or name CB )) or resid \ 798 through 815 or (resid 816 and (name N or name CA or name C or name O or nam \ e CB )) or resid 817 through 821 or (resid 822 and (name N or name CA or name C \ or name O or name CB )) or resid 823 through 830 or (resid 831 through 832 and ( \ name N or name CA or name C or name O or name CB )) or resid 833 through 1023 or \ (resid 1024 through 1047 and (name N or name CA or name C or name O or name CB \ )) or resid 1048 through 1092 or (resid 1093 through 1094 and (name N or name CA \ or name C or name O or name CB )) or resid 1095 through 1126 or (resid 1127 thr \ ough 1128 and (name N or name CA or name C or name O or name CB )) or resid 1129 \ through 1210 or (resid 1211 through 1212 and (name N or name CA or name C or na \ me O or name CB )) or resid 1213 through 1230 or (resid 1231 and (name N or name \ CA or name C or name O or name CB )) or resid 1232 through 1259 or (resid 1260 \ through 1261 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 262 through 1274 or (resid 1275 through 1276 and (name N or name CA or name C or \ name O or name CB )) or resid 1277 through 1298 or (resid 1299 through 1423 and \ (name N or name CA or name C or name O or name CB )) or resid 1424 through 1426 \ or (resid 1427 and (name N or name CA or name C or name O or name CB )) or resi \ d 1428 through 1467 or (resid 1468 and (name N or name CA or name C or name O or \ name CB )) or resid 1469 through 1482 or (resid 1483 through 1485 and (name N o \ r name CA or name C or name O or name CB )) or resid 1486 or (resid 1487 through \ 1489 and (name N or name CA or name C or name O or name CB )) or resid 1490 thr \ ough 1512 or (resid 1513 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1514 through 1525 or (resid 1526 and (name N or name CA or name C or \ name O or name CB )) or resid 1527 through 1536 or (resid 1537 and (name N or na \ me CA or name C or name O or name CB )) or resid 1538 through 1540 or (resid 154 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 1542 through \ 1578 or (resid 1579 and (name N or name CA or name C or name O or name CB )) or \ resid 1580 through 1595 or (resid 1596 and (name N or name CA or name C or name \ O or name CB )) or resid 1597 through 1628 or (resid 1629 and (name N or name C \ A or name C or name O or name CB )) or resid 1630 or (resid 1631 through 1632 an \ d (name N or name CA or name C or name O or name CB )) or resid 1633 through 164 \ 2 or (resid 1643 through 1644 and (name N or name CA or name C or name O or name \ CB )) or resid 1645 through 1648 or (resid 1649 and (name N or name CA or name \ C or name O or name CB )) or resid 1650 through 1808 or (resid 1809 through 1811 \ and (name N or name CA or name C or name O or name CB )) or resid 1812 through \ 1859 or (resid 1860 and (name N or name CA or name C or name O or name CB )) or \ resid 1861 through 1929 or (resid 1930 and (name N or name CA or name C or name \ O or name CB )) or resid 1931 through 2002 or (resid 2003 through 2004 and (name \ N or name CA or name C or name O or name CB )) or resid 2005 through 2012 or (r \ esid 2013 through 2021 and (name N or name CA or name C or name O or name CB )) \ or resid 2022 or (resid 2023 and (name N or name CA or name C or name O or name \ CB )) or resid 2024 through 2027 or (resid 2028 through 2029 and (name N or name \ CA or name C or name O or name CB )) or resid 2030 through 2031 or (resid 2032 \ through 2033 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 034 through 2045 or resid 2091 through 2107 or (resid 2108 through 2109 and (nam \ e N or name CA or name C or name O or name CB )) or resid 2110 through 2126 or ( \ resid 2127 and (name N or name CA or name C or name O or name CB )) or resid 212 \ 8 through 2156 or (resid 2157 and (name N or name CA or name C or name O or name \ CB )) or resid 2158 through 2173 or (resid 2174 through 2175 and (name N or nam \ e CA or name C or name O or name CB )) or resid 2176 through 2188 or (resid 2189 \ and (name N or name CA or name C or name O or name CB )) or resid 2190 through \ 2264 or (resid 2265 and (name N or name CA or name C or name O or name CB )) or \ resid 2266 through 2290 or (resid 2291 through 2292 and (name N or name CA or na \ me C or name O or name CB )) or resid 2293 through 2295 or (resid 2296 through 2 \ 297 and (name N or name CA or name C or name O or name CB )) or resid 2298 throu \ gh 2306 or (resid 2307 through 2309 and (name N or name CA or name C or name O o \ r name CB )) or resid 2310 through 2332 or (resid 2333 and (name N or name CA or \ name C or name O or name CB )) or resid 2334 through 2354 or (resid 2355 and (n \ ame N or name CA or name C or name O or name CB )) or resid 2356 through 2362 or \ (resid 2363 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 364 through 2422 or (resid 2423 and (name N or name CA or name C or name O or na \ me CB )) or resid 2424 through 2439 or (resid 2440 and (name N or name CA or nam \ e C or name O or name CB )) or resid 2441 through 2448 or (resid 2449 through 24 \ 50 and (name N or name CA or name C or name O or name CB )) or resid 2451 throug \ h 2465 or (resid 2466 and (name N or name CA or name C or name O or name CB )) o \ r resid 2467 through 2468 or (resid 2469 and (name N or name CA or name C or nam \ e O or name CB )) or resid 2470 through 2493 or (resid 2494 and (name N or name \ CA or name C or name O or name CB )) or resid 2495 through 2535 or (resid 2536 t \ hrough 2540 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 41 through 2547 or (resid 2548 through 2550 and (name N or name CA or name C or \ name O or name CB )) or resid 2551 through 2553 or (resid 2554 and (name N or na \ me CA or name C or name O or name CB )) or resid 2555 through 2558 or (resid 255 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 2560 through \ 2563 or (resid 2564 and (name N or name CA or name C or name O or name CB )) or \ resid 2565 through 2568 or (resid 2569 through 2570 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 2571 through 2576 and (name N or name CA \ or name C or name O or name CB )) or resid 2577 through 2578 or (resid 2579 thr \ ough 2580 and (name N or name CA or name C or name O or name CB )) or resid 2581 \ through 2593 or (resid 2594 through 2595 and (name N or name CA or name C or na \ me O or name CB )) or resid 2596 through 2600 or (resid 2601 and (name N or name \ CA or name C or name O or name CB )) or resid 2602 through 2606 or (resid 2607 \ through 2609 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 610 through 2627 or (resid 2628 through 2630 and (name N or name CA or name C or \ name O or name CB )) or resid 2631 through 2640 or (resid 2641 through 2644 and \ (name N or name CA or name C or name O or name CB )) or resid 2645 through 2653 \ or (resid 2654 through 2657 and (name N or name CA or name C or name O or name \ CB )) or resid 2658 through 2665 or (resid 2666 through 2667 and (name N or name \ CA or name C or name O or name CB )) or resid 2668 through 2673 or (resid 2674 \ and (name N or name CA or name C or name O or name CB )) or resid 2675 through 2 \ 961 or (resid 2962 through 2996 and (name N or name CA or name C or name O or na \ me CB )) or resid 2997 through 3009 or (resid 3010 through 3012 and (name N or n \ ame CA or name C or name O or name CB )) or resid 3013 through 3015 or (resid 30 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 3017 throug \ h 3018 or (resid 3019 through 3090 and (name N or name CA or name C or name O or \ name CB )) or (resid 3091 through 3190 and (name N or name CA or name C or name \ O or name CB )) or resid 3191 through 3379 or (resid 3396 through 3426 and (nam \ e N or name CA or name C or name O or name CB )) or resid 3427 through 3444 or ( \ resid 3445 through 3450 and (name N or name CA or name C or name O or name CB )) \ or resid 3451 through 3611 or (resid 3625 through 3627 and (name N or name CA o \ r name C or name O or name CB )) or resid 3628 through 3629 or (resid 3630 throu \ gh 3631 and (name N or name CA or name C or name O or name CB )) or resid 3632 t \ hrough 3709 or (resid 3710 and (name N or name CA or name C or name O or name CB \ )) or resid 3711 through 3731 or (resid 3732 and (name N or name CA or name C o \ r name O or name CB )) or resid 3733 or (resid 3734 through 3751 and (name N or \ name CA or name C or name O or name CB )) or resid 3752 through 3843 or (resid 3 \ 844 and (name N or name CA or name C or name O or name CB )) or resid 3845 throu \ gh 3926 or (resid 3927 and (name N or name CA or name C or name O or name CB )) \ or resid 3928 or (resid 3929 and (name N or name CA or name C or name O or name \ CB )) or resid 3930 through 3931 or (resid 3932 and (name N or name CA or name C \ or name O or name CB )) or resid 3933 through 3939 or (resid 3940 through 3941 \ and (name N or name CA or name C or name O or name CB )) or resid 3942 through 3 \ 952 or (resid 3953 through 3954 and (name N or name CA or name C or name O or na \ me CB )) or resid 3955 through 3983 or (resid 3984 and (name N or name CA or nam \ e C or name O or name CB )) or resid 3985 through 4001 or (resid 4002 and (name \ N or name CA or name C or name O or name CB )) or resid 4003 through 4013 or (re \ sid 4014 through 4015 and (name N or name CA or name C or name O or name CB )) o \ r resid 4016 through 4036 or (resid 4037 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 4038 through 4041 and (name N or name CA or name C o \ r name O or name CB )) or resid 4042 through 4062 or (resid 4063 and (name N or \ name CA or name C or name O or name CB )) or resid 4064 through 4065 or (resid 4 \ 066 and (name N or name CA or name C or name O or name CB )) or resid 4067 throu \ gh 4068 or (resid 4069 through 4070 and (name N or name CA or name C or name O o \ r name CB )) or resid 4071 through 4077 or (resid 4078 through 4079 and (name N \ or name CA or name C or name O or name CB )) or resid 4080 or (resid 4081 and (n \ ame N or name CA or name C or name O or name CB )) or resid 4082 through 4084 or \ (resid 4085 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 086 through 4087 or (resid 4088 and (name N or name CA or name C or name O or na \ me CB )) or resid 4089 through 4099 or (resid 4100 through 4102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 4103 through 4113 or (resid 41 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 4115 throug \ h 4130 or (resid 4131 and (name N or name CA or name C or name O or name CB )) o \ r resid 4132 through 4133 or (resid 4134 and (name N or name CA or name C or nam \ e O or name CB )) or resid 4135 through 4136 or (resid 4137 through 4138 and (na \ me N or name CA or name C or name O or name CB )) or resid 4139 through 4158 or \ (resid 4159 through 4162 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4163 through 4183 or (resid 4184 and (name N or name CA or name C or \ name O or name CB )) or (resid 4185 through 4191 and (name N or name CA or name \ C or name O or name CB )) or resid 4192 through 4229 or (resid 4230 through 4231 \ and (name N or name CA or name C or name O or name CB )) or resid 4232 through \ 4253 or (resid 4323 through 4328 and (name N or name CA or name C or name O or n \ ame CB )) or resid 4329 through 4673 or (resid 4674 through 4676 and (name N or \ name CA or name C or name O or name CB )) or resid 4677 through 4679 or (resid 4 \ 680 and (name N or name CA or name C or name O or name CB )) or resid 4681 throu \ gh 4717 or (resid 4718 and (name N or name CA or name C or name O or name CB )) \ or resid 4719 through 4722 or (resid 4723 and (name N or name CA or name C or na \ me O or name CB )) or resid 4724 through 4742 or (resid 4743 through 4746 and (n \ ame N or name CA or name C or name O or name CB )) or resid 4747 through 4753 or \ (resid 4754 through 4771 and (name N or name CA or name C or name O or name CB \ )) or resid 4772 through 4817 or (resid 4818 and (name N or name CA or name C or \ name O or name CB )) or resid 4819 through 4820 or (resid 4821 and (name N or n \ ame CA or name C or name O or name CB )) or resid 4822 through 4898 or (resid 48 \ 99 through 4900 and (name N or name CA or name C or name O or name CB )) or resi \ d 4901 through 4943 or (resid 4944 through 4945 and (name N or name CA or name C \ or name O or name CB )) or resid 4946 through 4952 or (resid 4953 through 4955 \ and (name N or name CA or name C or name O or name CB )) or resid 4956 through 4 \ 999 or (resid 5000 and (name N or name CA or name C or name O or name CB )) or r \ esid 5001 through 5006 or (resid 5007 and (name N or name CA or name C or name O \ or name CB )) or resid 5008 through 5028 or (resid 5029 through 5031 and (name \ N or name CA or name C or name O or name CB )) or resid 5032 through 5036 or res \ id 5101 through 5104)) } ncs_group { reference = (chain 'B' and (resid 1 through 5 or (resid 6 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 28 or (resid 29 and (name N \ or name CA or name C or name O or name CB )) or resid 30 or (resid 31 and (name \ N or name CA or name C or name O or name CB )) or resid 32 through 33 or (resid \ 34 through 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 37 or (resid 38 and (name N or name CA or name C or name O or name CB \ )) or resid 39 or (resid 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 65 or (resid 66 and (name N or name CA or name C or na \ me O or name CB )) or resid 67 through 84 or (resid 85 and (name N or name CA or \ name C or name O or name CB )) or resid 86 or (resid 87 and (name N or name CA \ or name C or name O or name CB )) or resid 88 through 99 or (resid 100 and (name \ N or name CA or name C or name O or name CB )) or resid 101 through 107)) selection = (chain 'E' and (resid 1 through 5 or (resid 6 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 14 or (resid 15 and (name N \ or name CA or name C or name O or name CB )) or resid 16 through 28 or (resid 29 \ and (name N or name CA or name C or name O or name CB )) or resid 30 or (resid \ 31 and (name N or name CA or name C or name O or name CB )) or resid 32 through \ 33 or (resid 34 through 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 39 or (resid 40 and (name N or name CA or name C or name \ O or name CB )) or resid 41 through 76 or (resid 77 and (name N or name CA or n \ ame C or name O or name CB )) or resid 78 through 84 or (resid 85 and (name N or \ name CA or name C or name O or name CB )) or resid 86 through 99 or (resid 100 \ and (name N or name CA or name C or name O or name CB )) or resid 101 through 10 \ 7)) selection = (chain 'H' and (resid 1 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 14 or (resid 15 and (name N or name CA \ or name C or name O or name CB )) or resid 16 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 33 or (res \ id 34 through 35 and (name N or name CA or name C or name O or name CB )) or res \ id 36 or (resid 37 through 38 and (name N or name CA or name C or name O or name \ CB )) or resid 39 or (resid 40 and (name N or name CA or name C or name O or na \ me CB )) or resid 41 through 76 or (resid 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 86 or (resid 87 and (name N or name CA \ or name C or name O or name CB )) or resid 88 through 99 or (resid 100 and (nam \ e N or name CA or name C or name O or name CB )) or resid 101 through 107)) selection = (chain 'K' and (resid 1 through 5 or (resid 6 through 8 and (name N or name CA o \ r name C or name O or name CB )) or resid 9 through 14 or (resid 15 and (name N \ or name CA or name C or name O or name CB )) or resid 16 through 37 or (resid 38 \ and (name N or name CA or name C or name O or name CB )) or resid 39 through 65 \ or (resid 66 and (name N or name CA or name C or name O or name CB )) or resid \ 67 through 76 or (resid 77 and (name N or name CA or name C or name O or name CB \ )) or resid 78 through 84 or (resid 85 and (name N or name CA or name C or name \ O or name CB )) or resid 86 or (resid 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 107)) } ncs_group { reference = (chain 'C' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 6 or (resid 7 through 9 and (name N or \ name CA or name C or name O or name CB )) or resid 10 through 72 or (resid 73 t \ hrough 96 and (name N or name CA or name C or name O or name CB )) or resid 97 t \ hrough 128 or resid 135 through 148)) selection = (chain 'F' and (resid 1 through 68 or (resid 69 and (name N or name CA or name C \ or name O or name CB )) or resid 70 through 128 or resid 135 through 148)) selection = (chain 'I' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 6 or (resid 7 through 9 and (name N or \ name CA or name C or name O or name CB )) or resid 10 through 12 or (resid 13 t \ hrough 16 and (name N or name CA or name C or name O or name CB )) or resid 17 t \ hrough 27 or (resid 28 through 33 and (name N or name CA or name C or name O or \ name CB )) or resid 34 through 128 or resid 135 through 148)) selection = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 6 or (resid 7 through 9 and (name N or \ name CA or name C or name O or name CB )) or resid 10 through 36 or (resid 37 t \ hrough 40 and (name N or name CA or name C or name O or name CB )) or (resid 41 \ through 56 and (name N or name CA or name C or name O or name CB )) or resid 62 \ through 72 or (resid 73 through 96 and (name N or name CA or name C or name O or \ name CB )) or (resid 97 through 128 and (name N or name CA or name C or name O \ or name CB )) or resid 135 through 148)) } 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: 4.710 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: 0.060 Extract box with map and model: 28.770 Check model and map are aligned: 1.230 Set scattering table: 0.780 Process input model: 324.730 Find NCS groups from input model: 11.750 Set up NCS constraints: 0.460 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 375.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.003 0.070 116571 Z= 0.205 Angle : 0.633 13.544 159543 Z= 0.371 Chirality : 0.040 0.340 19149 Planarity : 0.004 0.070 20607 Dihedral : 12.170 89.162 36531 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.69 % Favored : 98.29 % Rotamer: Outliers : 0.63 % Allowed : 0.59 % Favored : 98.78 % Cbeta Deviations : 0.00 % 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: 1.70 (0.07), residues: 16359 helix: 2.21 (0.05), residues: 8904 sheet: -0.29 (0.14), residues: 1443 loop : -0.12 (0.08), residues: 6012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP D1143 HIS 0.015 0.001 HIS D 113 PHE 0.040 0.002 PHE A3992 TYR 0.036 0.002 TYR D3934 ARG 0.021 0.000 ARG D1131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1115 time to evaluate : 10.483 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: D 2198 MET cc_start: 0.8809 (mmm) cc_final: 0.8514 (mmp) REVERT: D 2680 TRP cc_start: 0.7529 (m-10) cc_final: 0.7184 (m100) REVERT: D 2700 MET cc_start: 0.8540 (ppp) cc_final: 0.8302 (ppp) REVERT: D 3673 MET cc_start: 0.8050 (mtm) cc_final: 0.7766 (ttm) REVERT: D 3728 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9070 (mp) REVERT: D 4047 MET cc_start: 0.8618 (tmm) cc_final: 0.8370 (tmm) REVERT: D 4245 MET cc_start: 0.8856 (mtp) cc_final: 0.8559 (mmt) REVERT: D 4567 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8877 (tt) REVERT: D 4581 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7955 (ttpp) REVERT: A 334 MET cc_start: 0.7740 (mmm) cc_final: 0.7452 (mmm) REVERT: A 2250 MET cc_start: 0.8711 (tpp) cc_final: 0.8433 (tpp) REVERT: A 2347 GLU cc_start: 0.6934 (tp30) cc_final: 0.6715 (tp30) REVERT: A 3673 MET cc_start: 0.8004 (mtm) cc_final: 0.7624 (ttm) REVERT: G 1286 MET cc_start: 0.7545 (mmm) cc_final: 0.7293 (tpt) REVERT: G 1494 MET cc_start: 0.8141 (mtp) cc_final: 0.7811 (mtp) REVERT: G 3729 MET cc_start: 0.8663 (mtt) cc_final: 0.8333 (mtm) REVERT: G 4639 MET cc_start: 0.8046 (ttm) cc_final: 0.7794 (ttm) REVERT: J 1283 LEU cc_start: 0.7995 (tt) cc_final: 0.7740 (mm) REVERT: J 1944 GLU cc_start: 0.7799 (tt0) cc_final: 0.7506 (tm-30) REVERT: J 2546 MET cc_start: 0.7814 (tpp) cc_final: 0.7547 (tpt) REVERT: J 3875 MET cc_start: 0.8423 (mmm) cc_final: 0.8178 (mmp) outliers start: 56 outliers final: 16 residues processed: 1162 average time/residue: 0.8544 time to fit residues: 1802.7840 Evaluate side-chains 817 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 798 time to evaluate : 9.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1426 ILE Chi-restraints excluded: chain D residue 2503 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2563 THR Chi-restraints excluded: chain D residue 2577 ILE Chi-restraints excluded: chain D residue 2581 SER Chi-restraints excluded: chain D residue 3721 LEU Chi-restraints excluded: chain D residue 3728 ILE Chi-restraints excluded: chain D residue 4567 LEU Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain G residue 3674 ILE Chi-restraints excluded: chain G residue 3721 LEU Chi-restraints excluded: chain G residue 3763 LEU Chi-restraints excluded: chain G residue 3768 SER Chi-restraints excluded: chain G residue 4792 LEU Chi-restraints excluded: chain G residue 4796 MET Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 1408 optimal weight: 6.9990 chunk 1264 optimal weight: 6.9990 chunk 701 optimal weight: 30.0000 chunk 431 optimal weight: 10.0000 chunk 852 optimal weight: 20.0000 chunk 675 optimal weight: 20.0000 chunk 1307 optimal weight: 5.9990 chunk 505 optimal weight: 7.9990 chunk 794 optimal weight: 0.1980 chunk 973 optimal weight: 8.9990 chunk 1514 optimal weight: 30.0000 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS D 465 GLN D 502 HIS D1231 GLN ** D1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1571 ASN D1696 HIS D1973 GLN ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2161 GLN ** D2420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2515 GLN ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3950 ASN ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4553 ASN ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4857 ASN E 25 HIS A 218 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 617 ASN A 624 ASN A1563 GLN ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 HIS A2193 GLN A2551 ASN A3901 ASN ** A4153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4204 GLN A4574 ASN A4650 HIS A4803 HIS A4806 ASN G 190 GLN ** G 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1640 HIS G2003 GLN ** G2005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2007 ASN G2032 GLN G2036 GLN ** G2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2515 GLN G2647 HIS G3766 GLN G3970 GLN G4009 GLN G4558 ASN ** G4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 HIS J 23 GLN ** J 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 GLN ** J 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 705 ASN ** J 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1127 HIS J1254 HIS ** J1298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1953 HIS J2107 GLN ** J2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2284 ASN ** J2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J2599 GLN ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS J3998 HIS J4153 HIS J4201 ASN J4714 ASN ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 116571 Z= 0.420 Angle : 0.648 11.181 159543 Z= 0.340 Chirality : 0.040 0.176 19149 Planarity : 0.004 0.067 20607 Dihedral : 4.749 88.072 17706 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.41 % Allowed : 8.98 % Favored : 89.61 % Cbeta Deviations : 0.00 % 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: 1.54 (0.07), residues: 16359 helix: 2.11 (0.05), residues: 9042 sheet: -0.62 (0.13), residues: 1472 loop : -0.21 (0.08), residues: 5845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D1143 HIS 0.011 0.002 HIS D4978 PHE 0.033 0.002 PHE D2997 TYR 0.021 0.002 TYR A3968 ARG 0.007 0.001 ARG G3773 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 778 time to evaluate : 9.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1494 MET cc_start: 0.8053 (mtp) cc_final: 0.7475 (mtm) REVERT: D 2211 MET cc_start: 0.7770 (tmm) cc_final: 0.7441 (tmm) REVERT: D 2680 TRP cc_start: 0.7615 (m-10) cc_final: 0.7275 (m100) REVERT: D 3673 MET cc_start: 0.8281 (mtm) cc_final: 0.7764 (ttm) REVERT: D 3728 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9201 (mp) REVERT: D 3782 MET cc_start: 0.8389 (ttm) cc_final: 0.7977 (ttm) REVERT: D 3899 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8701 (t80) REVERT: D 4047 MET cc_start: 0.8762 (tmm) cc_final: 0.8378 (tmm) REVERT: D 4064 MET cc_start: 0.7907 (mtm) cc_final: 0.7602 (mmm) REVERT: D 4632 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7994 (tp) REVERT: D 4917 ASP cc_start: 0.7592 (t0) cc_final: 0.7375 (t0) REVERT: E 102 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 131 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 334 MET cc_start: 0.8042 (mmm) cc_final: 0.7574 (mmm) REVERT: A 2250 MET cc_start: 0.8905 (tpp) cc_final: 0.8698 (tpp) REVERT: A 3999 MET cc_start: 0.8789 (mmm) cc_final: 0.8583 (mmm) REVERT: G 334 MET cc_start: 0.7299 (tpp) cc_final: 0.6814 (tpp) REVERT: G 403 MET cc_start: 0.9169 (mmt) cc_final: 0.8757 (mmt) REVERT: G 1286 MET cc_start: 0.7951 (mmm) cc_final: 0.7618 (tpt) REVERT: G 1494 MET cc_start: 0.8434 (mtp) cc_final: 0.8130 (mtp) REVERT: G 1929 MET cc_start: 0.8499 (ttm) cc_final: 0.8284 (ttt) REVERT: G 2198 MET cc_start: 0.9079 (mmm) cc_final: 0.8743 (tpp) REVERT: G 3652 MET cc_start: 0.8860 (mpp) cc_final: 0.8415 (mpp) REVERT: G 4631 PHE cc_start: 0.8630 (t80) cc_final: 0.8385 (t80) REVERT: G 4639 MET cc_start: 0.8092 (ttm) cc_final: 0.7857 (ttm) REVERT: G 4883 TYR cc_start: 0.9054 (t80) cc_final: 0.8746 (t80) REVERT: G 4887 MET cc_start: 0.8644 (tpp) cc_final: 0.8424 (ttm) REVERT: J 1283 LEU cc_start: 0.8233 (tt) cc_final: 0.7841 (mm) REVERT: J 3673 MET cc_start: 0.8104 (tmm) cc_final: 0.7839 (tmm) REVERT: J 4687 TYR cc_start: 0.7842 (m-80) cc_final: 0.7637 (m-80) REVERT: J 4967 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.7315 (t80) REVERT: J 4993 MET cc_start: 0.7410 (ttp) cc_final: 0.7074 (tmm) REVERT: L 1 MET cc_start: 0.6519 (ttm) cc_final: 0.6016 (ttt) outliers start: 126 outliers final: 74 residues processed: 864 average time/residue: 0.8451 time to fit residues: 1336.9389 Evaluate side-chains 818 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 739 time to evaluate : 9.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 506 TYR Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1573 MET Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2178 MET Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2503 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 3728 ILE Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 4017 LEU Chi-restraints excluded: chain D residue 4560 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4767 TRP Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2275 VAL Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3836 MET Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 3929 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4931 ILE Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain A residue 5027 CYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 1123 VAL Chi-restraints excluded: chain G residue 1839 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2332 LEU Chi-restraints excluded: chain G residue 2460 LEU Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3675 ASP Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3803 SER Chi-restraints excluded: chain G residue 4147 LEU Chi-restraints excluded: chain G residue 4184 MET Chi-restraints excluded: chain G residue 4792 LEU Chi-restraints excluded: chain G residue 4926 VAL Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 113 HIS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 2302 LEU Chi-restraints excluded: chain J residue 2518 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 2569 PHE Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3798 LEU Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4879 MET Chi-restraints excluded: chain J residue 4967 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 841 optimal weight: 0.7980 chunk 470 optimal weight: 2.9990 chunk 1260 optimal weight: 9.9990 chunk 1031 optimal weight: 0.0870 chunk 417 optimal weight: 10.0000 chunk 1517 optimal weight: 50.0000 chunk 1639 optimal weight: 8.9990 chunk 1351 optimal weight: 30.0000 chunk 1504 optimal weight: 7.9990 chunk 517 optimal weight: 9.9990 chunk 1217 optimal weight: 0.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS ** D1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1640 HIS D1972 ASN D2420 HIS D3897 ASN ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4558 ASN ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4054 ASN A4153 HIS A4201 ASN B 25 HIS ** G 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2005 GLN G2161 GLN G2176 ASN G2180 GLN ** G2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3889 GLN G4574 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 HIS J 138 GLN J 151 HIS J 197 GLN ** J 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1298 HIS ** J1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS K 43 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 116571 Z= 0.222 Angle : 0.515 10.257 159543 Z= 0.267 Chirality : 0.037 0.211 19149 Planarity : 0.003 0.067 20607 Dihedral : 4.492 88.117 17682 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.56 % Allowed : 11.61 % Favored : 86.83 % Cbeta Deviations : 0.00 % 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: 1.76 (0.07), residues: 16359 helix: 2.33 (0.05), residues: 9036 sheet: -0.63 (0.13), residues: 1494 loop : -0.16 (0.08), residues: 5829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A4716 HIS 0.007 0.001 HIS J3771 PHE 0.032 0.001 PHE A4093 TYR 0.044 0.001 TYR A3968 ARG 0.004 0.000 ARG G5017 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 779 time to evaluate : 9.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1494 MET cc_start: 0.8038 (mtp) cc_final: 0.7542 (mtm) REVERT: D 2198 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8374 (mmm) REVERT: D 2211 MET cc_start: 0.7756 (tmm) cc_final: 0.7473 (tmm) REVERT: D 2680 TRP cc_start: 0.7609 (m-10) cc_final: 0.7271 (m100) REVERT: D 3673 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7607 (ttm) REVERT: D 3728 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9179 (mp) REVERT: D 3782 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7851 (ttm) REVERT: D 3899 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8683 (t80) REVERT: D 4047 MET cc_start: 0.8801 (tmm) cc_final: 0.8380 (tmm) REVERT: D 4064 MET cc_start: 0.7902 (mtm) cc_final: 0.7626 (mmm) REVERT: D 4917 ASP cc_start: 0.7559 (t0) cc_final: 0.7249 (t0) REVERT: A 334 MET cc_start: 0.7990 (mmm) cc_final: 0.7700 (mmm) REVERT: B 25 HIS cc_start: 0.8900 (OUTLIER) cc_final: 0.8110 (m-70) REVERT: G 403 MET cc_start: 0.9128 (mmt) cc_final: 0.8794 (mmt) REVERT: G 1286 MET cc_start: 0.7990 (mmm) cc_final: 0.7668 (tpt) REVERT: G 1494 MET cc_start: 0.8408 (mtp) cc_final: 0.8101 (mtp) REVERT: G 1636 MET cc_start: 0.8246 (ppp) cc_final: 0.8029 (ppp) REVERT: G 1929 MET cc_start: 0.8531 (ttm) cc_final: 0.8328 (ttt) REVERT: G 2698 MET cc_start: 0.8685 (tmm) cc_final: 0.8353 (tmm) REVERT: G 3652 MET cc_start: 0.8880 (mpp) cc_final: 0.8393 (mpp) REVERT: G 3723 MET cc_start: 0.8572 (mmm) cc_final: 0.8106 (mmt) REVERT: G 4796 MET cc_start: 0.8961 (tpp) cc_final: 0.8704 (tpp) REVERT: J 1283 LEU cc_start: 0.8277 (tt) cc_final: 0.7817 (mm) REVERT: J 1494 MET cc_start: 0.7009 (mtm) cc_final: 0.6247 (mtm) REVERT: J 3673 MET cc_start: 0.8060 (tmm) cc_final: 0.7730 (tmm) REVERT: J 4097 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8475 (mtm) REVERT: J 4954 MET cc_start: 0.7300 (tmm) cc_final: 0.7022 (tmm) REVERT: J 4993 MET cc_start: 0.7373 (ttp) cc_final: 0.7045 (tmm) REVERT: L 1 MET cc_start: 0.6650 (ttm) cc_final: 0.6155 (ttt) outliers start: 139 outliers final: 89 residues processed: 877 average time/residue: 0.8502 time to fit residues: 1366.3484 Evaluate side-chains 844 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 748 time to evaluate : 9.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 506 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2178 MET Chi-restraints excluded: chain D residue 2198 MET Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2356 LEU Chi-restraints excluded: chain D residue 2503 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 3728 ILE Chi-restraints excluded: chain D residue 3782 MET Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 4019 LEU Chi-restraints excluded: chain D residue 4767 TRP Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4914 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1839 VAL Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2275 VAL Chi-restraints excluded: chain A residue 2554 LEU Chi-restraints excluded: chain A residue 2558 VAL Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 3929 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2280 VAL Chi-restraints excluded: chain G residue 2332 LEU Chi-restraints excluded: chain G residue 2354 VAL Chi-restraints excluded: chain G residue 2460 LEU Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3675 ASP Chi-restraints excluded: chain G residue 3803 SER Chi-restraints excluded: chain G residue 4184 MET Chi-restraints excluded: chain G residue 4792 LEU Chi-restraints excluded: chain G residue 4926 VAL Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 113 HIS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 607 CYS Chi-restraints excluded: chain J residue 1519 LEU Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1939 MET Chi-restraints excluded: chain J residue 2135 LEU Chi-restraints excluded: chain J residue 2302 LEU Chi-restraints excluded: chain J residue 2506 LEU Chi-restraints excluded: chain J residue 2518 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 2569 PHE Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3892 CYS Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4097 MET Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4879 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 1499 optimal weight: 7.9990 chunk 1140 optimal weight: 0.8980 chunk 787 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 724 optimal weight: 8.9990 chunk 1018 optimal weight: 4.9990 chunk 1522 optimal weight: 0.0010 chunk 1612 optimal weight: 9.9990 chunk 795 optimal weight: 9.9990 chunk 1443 optimal weight: 0.0070 chunk 434 optimal weight: 1.9990 overall best weight: 1.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 ASN ** D1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4054 ASN ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4553 ASN ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS A4857 ASN B 25 HIS B 70 GLN ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2260 ASN J 113 HIS ** J 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J2584 HIS ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS J4574 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 116571 Z= 0.170 Angle : 0.486 10.989 159543 Z= 0.250 Chirality : 0.037 0.326 19149 Planarity : 0.003 0.068 20607 Dihedral : 4.327 88.401 17682 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.95 % Allowed : 12.91 % Favored : 85.14 % Cbeta Deviations : 0.00 % 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: 1.92 (0.07), residues: 16359 helix: 2.47 (0.05), residues: 9042 sheet: -0.61 (0.13), residues: 1497 loop : -0.11 (0.08), residues: 5820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A4716 HIS 0.017 0.001 HIS B 25 PHE 0.033 0.001 PHE A4093 TYR 0.051 0.001 TYR A3968 ARG 0.004 0.000 ARG G5017 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 790 time to evaluate : 9.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 667 MET cc_start: 0.7112 (ppp) cc_final: 0.6842 (ppp) REVERT: D 1494 MET cc_start: 0.7990 (mtp) cc_final: 0.7663 (mtm) REVERT: D 2198 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8399 (mmm) REVERT: D 2211 MET cc_start: 0.7750 (tmm) cc_final: 0.7478 (tmm) REVERT: D 2680 TRP cc_start: 0.7616 (m-10) cc_final: 0.7276 (m100) REVERT: D 3673 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7675 (ttm) REVERT: D 3728 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9160 (mp) REVERT: D 3782 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7793 (ttm) REVERT: D 3899 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8634 (t80) REVERT: D 4047 MET cc_start: 0.8834 (tmm) cc_final: 0.8444 (tmm) REVERT: D 4064 MET cc_start: 0.7961 (mtm) cc_final: 0.7706 (mpp) REVERT: D 4917 ASP cc_start: 0.7470 (t0) cc_final: 0.7152 (t0) REVERT: D 4989 MET cc_start: 0.7734 (tmm) cc_final: 0.7443 (tmm) REVERT: A 334 MET cc_start: 0.7949 (mmm) cc_final: 0.7565 (mmm) REVERT: A 341 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.6700 (t80) REVERT: A 3820 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8747 (tt) REVERT: A 3889 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: B 25 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8148 (m-70) REVERT: G 403 MET cc_start: 0.9118 (mmt) cc_final: 0.8882 (mmt) REVERT: G 1286 MET cc_start: 0.7999 (mmm) cc_final: 0.7678 (tpt) REVERT: G 1636 MET cc_start: 0.8321 (ppp) cc_final: 0.7988 (ppp) REVERT: G 2698 MET cc_start: 0.8661 (tmm) cc_final: 0.8301 (tmm) REVERT: G 3652 MET cc_start: 0.8892 (mpp) cc_final: 0.8395 (mpp) REVERT: G 3951 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8349 (t80) REVERT: G 3999 MET cc_start: 0.9191 (tpp) cc_final: 0.8816 (mmm) REVERT: G 4031 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8169 (mm) REVERT: G 4639 MET cc_start: 0.8087 (ttm) cc_final: 0.7830 (ttm) REVERT: G 4796 MET cc_start: 0.9003 (tpp) cc_final: 0.8700 (tpp) REVERT: G 4839 MET cc_start: 0.9218 (mmt) cc_final: 0.8985 (mmp) REVERT: G 4883 TYR cc_start: 0.8938 (t80) cc_final: 0.8673 (t80) REVERT: J 1494 MET cc_start: 0.6999 (mtm) cc_final: 0.6433 (mtm) REVERT: J 2242 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8790 (mt) REVERT: J 3673 MET cc_start: 0.7997 (tmm) cc_final: 0.7640 (tmm) REVERT: J 3805 LEU cc_start: 0.9210 (tp) cc_final: 0.9002 (tp) REVERT: J 4773 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.9019 (m) REVERT: J 4954 MET cc_start: 0.7330 (tmm) cc_final: 0.6904 (tmm) REVERT: J 4967 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.7370 (t80) REVERT: J 4993 MET cc_start: 0.7343 (ttp) cc_final: 0.7004 (tmm) REVERT: K 43 ASN cc_start: 0.8522 (m-40) cc_final: 0.8284 (m-40) REVERT: L 1 MET cc_start: 0.6743 (ttm) cc_final: 0.6239 (ttt) outliers start: 174 outliers final: 107 residues processed: 915 average time/residue: 0.8346 time to fit residues: 1401.3984 Evaluate side-chains 880 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 759 time to evaluate : 9.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 506 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1189 LEU Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1767 VAL Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2178 MET Chi-restraints excluded: chain D residue 2198 MET Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2356 LEU Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2563 THR Chi-restraints excluded: chain D residue 2581 SER Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 3728 ILE Chi-restraints excluded: chain D residue 3782 MET Chi-restraints excluded: chain D residue 3897 ASN Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 4010 ILE Chi-restraints excluded: chain D residue 4019 LEU Chi-restraints excluded: chain D residue 4839 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4914 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 2120 MET Chi-restraints excluded: chain A residue 2554 LEU Chi-restraints excluded: chain A residue 2558 VAL Chi-restraints excluded: chain A residue 2578 MET Chi-restraints excluded: chain A residue 3820 LEU Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3889 GLN Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 3929 SER Chi-restraints excluded: chain A residue 4081 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4827 LEU Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1597 VAL Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2280 VAL Chi-restraints excluded: chain G residue 2354 VAL Chi-restraints excluded: chain G residue 2460 LEU Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3803 SER Chi-restraints excluded: chain G residue 3899 PHE Chi-restraints excluded: chain G residue 3951 PHE Chi-restraints excluded: chain G residue 4029 SER Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4184 MET Chi-restraints excluded: chain G residue 4926 VAL Chi-restraints excluded: chain G residue 4936 ILE Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 1083 VAL Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1519 LEU Chi-restraints excluded: chain J residue 1561 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1953 HIS Chi-restraints excluded: chain J residue 2135 LEU Chi-restraints excluded: chain J residue 2242 ILE Chi-restraints excluded: chain J residue 2302 LEU Chi-restraints excluded: chain J residue 2506 LEU Chi-restraints excluded: chain J residue 2518 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 2569 PHE Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3892 CYS Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4036 VAL Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4754 ASN Chi-restraints excluded: chain J residue 4773 VAL Chi-restraints excluded: chain J residue 4931 ILE Chi-restraints excluded: chain J residue 4967 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 1342 optimal weight: 50.0000 chunk 915 optimal weight: 50.0000 chunk 23 optimal weight: 4.9990 chunk 1200 optimal weight: 30.0000 chunk 665 optimal weight: 50.0000 chunk 1375 optimal weight: 20.0000 chunk 1114 optimal weight: 40.0000 chunk 1 optimal weight: 10.0000 chunk 823 optimal weight: 30.0000 chunk 1447 optimal weight: 5.9990 chunk 406 optimal weight: 50.0000 overall best weight: 14.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D1491 ASN ** D1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1571 ASN D1610 ASN D1683 HIS ** D1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2169 GLN ** D3647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3901 ASN D4009 GLN D4054 ASN ** D4153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS A 412 ASN A 461 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS A 797 HIS ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2647 HIS A2673 HIS A3781 GLN A3814 GLN A3895 HIS ** A3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4020 GLN A4857 ASN A4886 HIS A4947 GLN B 70 GLN ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G3734 HIS G4020 GLN ** G4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 848 HIS ** J1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J2169 GLN ** J2193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2349 ASN ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS ** J4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J4209 GLN ** J4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.119 116571 Z= 0.996 Angle : 1.069 16.247 159543 Z= 0.553 Chirality : 0.051 0.331 19149 Planarity : 0.007 0.080 20607 Dihedral : 5.719 79.401 17679 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 3.86 % Allowed : 15.66 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.14 (0.06), residues: 16359 helix: 0.76 (0.05), residues: 9045 sheet: -1.35 (0.13), residues: 1454 loop : -1.00 (0.08), residues: 5860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP G1132 HIS 0.020 0.003 HIS D4978 PHE 0.041 0.004 PHE D2340 TYR 0.043 0.004 TYR A3968 ARG 0.012 0.001 ARG G 683 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 699 time to evaluate : 9.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 541 SER cc_start: 0.7922 (m) cc_final: 0.7435 (t) REVERT: D 846 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8606 (pp) REVERT: D 1286 MET cc_start: 0.7647 (tpt) cc_final: 0.7436 (tpt) REVERT: D 1491 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8982 (p0) REVERT: D 2198 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8709 (mmm) REVERT: D 2211 MET cc_start: 0.8056 (tmm) cc_final: 0.7643 (tmm) REVERT: D 2680 TRP cc_start: 0.7897 (m-10) cc_final: 0.7527 (m100) REVERT: D 3673 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8024 (ttm) REVERT: D 3769 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8846 (ttm170) REVERT: D 3899 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8744 (t80) REVERT: D 3943 ILE cc_start: 0.7285 (tp) cc_final: 0.7037 (tp) REVERT: D 3962 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8624 (m-80) REVERT: D 4047 MET cc_start: 0.8956 (tmm) cc_final: 0.8519 (tmm) REVERT: D 4064 MET cc_start: 0.8224 (mtm) cc_final: 0.7961 (mmp) REVERT: D 4874 MET cc_start: 0.8218 (mmp) cc_final: 0.8014 (mmp) REVERT: D 4989 MET cc_start: 0.8295 (tmm) cc_final: 0.7919 (tmm) REVERT: A 113 HIS cc_start: 0.9012 (OUTLIER) cc_final: 0.8527 (t70) REVERT: A 334 MET cc_start: 0.8058 (mmm) cc_final: 0.7855 (mmm) REVERT: A 2211 MET cc_start: 0.7553 (ttm) cc_final: 0.7342 (ttm) REVERT: A 2618 MET cc_start: 0.8592 (mmt) cc_final: 0.8214 (mmt) REVERT: A 3673 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8208 (ttm) REVERT: A 3899 PHE cc_start: 0.9485 (OUTLIER) cc_final: 0.9189 (m-80) REVERT: A 4639 MET cc_start: 0.8767 (mmp) cc_final: 0.8444 (mmp) REVERT: A 4716 TRP cc_start: 0.8716 (p-90) cc_final: 0.8460 (p-90) REVERT: G 35 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8182 (pp) REVERT: G 280 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9251 (pp) REVERT: G 540 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.9130 (t80) REVERT: G 1286 MET cc_start: 0.8134 (mmm) cc_final: 0.7539 (tpt) REVERT: G 1636 MET cc_start: 0.8509 (ppp) cc_final: 0.8109 (ppp) REVERT: G 2265 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8101 (pp) REVERT: G 3652 MET cc_start: 0.8967 (mpp) cc_final: 0.8632 (mpp) REVERT: G 3951 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.8972 (t80) REVERT: G 3999 MET cc_start: 0.9450 (tpp) cc_final: 0.9039 (mmm) REVERT: G 4245 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8570 (mtp) REVERT: J 42 PHE cc_start: 0.7718 (m-10) cc_final: 0.7497 (m-10) REVERT: J 180 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8549 (tp) REVERT: J 181 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7389 (p-80) REVERT: J 540 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: J 1494 MET cc_start: 0.7552 (mtm) cc_final: 0.6925 (mtm) REVERT: J 1636 MET cc_start: 0.7155 (ppp) cc_final: 0.6866 (tmm) REVERT: J 3673 MET cc_start: 0.8349 (tmm) cc_final: 0.8028 (tmm) REVERT: J 4026 MET cc_start: 0.8882 (tmm) cc_final: 0.8583 (tmm) REVERT: J 4097 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8619 (mtm) REVERT: J 4967 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7480 (t80) REVERT: J 4993 MET cc_start: 0.7592 (ttp) cc_final: 0.7124 (tmm) REVERT: J 5013 MET cc_start: 0.9058 (tpp) cc_final: 0.8761 (tpp) REVERT: K 43 ASN cc_start: 0.8735 (m-40) cc_final: 0.8371 (m-40) outliers start: 345 outliers final: 209 residues processed: 980 average time/residue: 0.8505 time to fit residues: 1533.7856 Evaluate side-chains 910 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 680 time to evaluate : 9.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 537 CYS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1235 THR Chi-restraints excluded: chain D residue 1283 LEU Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1491 ASN Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1617 THR Chi-restraints excluded: chain D residue 1648 MET Chi-restraints excluded: chain D residue 1666 THR Chi-restraints excluded: chain D residue 1736 VAL Chi-restraints excluded: chain D residue 1760 HIS Chi-restraints excluded: chain D residue 1767 VAL Chi-restraints excluded: chain D residue 1841 VAL Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2008 MET Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2178 MET Chi-restraints excluded: chain D residue 2198 MET Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2356 LEU Chi-restraints excluded: chain D residue 2503 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2563 THR Chi-restraints excluded: chain D residue 2581 SER Chi-restraints excluded: chain D residue 2700 MET Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 3721 LEU Chi-restraints excluded: chain D residue 3769 ARG Chi-restraints excluded: chain D residue 3897 ASN Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3907 THR Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3962 PHE Chi-restraints excluded: chain D residue 3969 ILE Chi-restraints excluded: chain D residue 4017 LEU Chi-restraints excluded: chain D residue 4080 TYR Chi-restraints excluded: chain D residue 4181 ILE Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4767 TRP Chi-restraints excluded: chain D residue 4792 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1636 MET Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1839 VAL Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2120 MET Chi-restraints excluded: chain A residue 2162 ILE Chi-restraints excluded: chain A residue 2275 VAL Chi-restraints excluded: chain A residue 2460 LEU Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2558 VAL Chi-restraints excluded: chain A residue 2643 LEU Chi-restraints excluded: chain A residue 2673 HIS Chi-restraints excluded: chain A residue 3639 THR Chi-restraints excluded: chain A residue 3646 THR Chi-restraints excluded: chain A residue 3673 MET Chi-restraints excluded: chain A residue 3674 ILE Chi-restraints excluded: chain A residue 3764 LEU Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3836 MET Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 3929 SER Chi-restraints excluded: chain A residue 3966 THR Chi-restraints excluded: chain A residue 4024 VAL Chi-restraints excluded: chain A residue 4081 VAL Chi-restraints excluded: chain A residue 4088 ILE Chi-restraints excluded: chain A residue 4123 ILE Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4813 LEU Chi-restraints excluded: chain A residue 4827 LEU Chi-restraints excluded: chain A residue 4858 PHE Chi-restraints excluded: chain A residue 4917 ASP Chi-restraints excluded: chain A residue 4918 ILE Chi-restraints excluded: chain A residue 4924 VAL Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4935 LEU Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4985 LEU Chi-restraints excluded: chain A residue 5013 MET Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 631 LEU Chi-restraints excluded: chain G residue 635 THR Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 663 TYR Chi-restraints excluded: chain G residue 716 PHE Chi-restraints excluded: chain G residue 1123 VAL Chi-restraints excluded: chain G residue 1149 VAL Chi-restraints excluded: chain G residue 1158 ASN Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1492 CYS Chi-restraints excluded: chain G residue 1715 LEU Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1839 VAL Chi-restraints excluded: chain G residue 1939 MET Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2123 LEU Chi-restraints excluded: chain G residue 2265 LEU Chi-restraints excluded: chain G residue 2273 LEU Chi-restraints excluded: chain G residue 2275 VAL Chi-restraints excluded: chain G residue 2354 VAL Chi-restraints excluded: chain G residue 2583 LEU Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3656 SER Chi-restraints excluded: chain G residue 3675 ASP Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3782 MET Chi-restraints excluded: chain G residue 3790 THR Chi-restraints excluded: chain G residue 3803 SER Chi-restraints excluded: chain G residue 3899 PHE Chi-restraints excluded: chain G residue 3951 PHE Chi-restraints excluded: chain G residue 3966 THR Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4035 VAL Chi-restraints excluded: chain G residue 4045 VAL Chi-restraints excluded: chain G residue 4221 VAL Chi-restraints excluded: chain G residue 4223 ASN Chi-restraints excluded: chain G residue 4241 THR Chi-restraints excluded: chain G residue 4245 MET Chi-restraints excluded: chain G residue 4554 TYR Chi-restraints excluded: chain G residue 4565 LEU Chi-restraints excluded: chain G residue 4743 MET Chi-restraints excluded: chain G residue 4816 ILE Chi-restraints excluded: chain G residue 4853 VAL Chi-restraints excluded: chain G residue 4936 ILE Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 181 HIS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 540 PHE Chi-restraints excluded: chain J residue 607 CYS Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 789 VAL Chi-restraints excluded: chain J residue 1083 VAL Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1679 ASN Chi-restraints excluded: chain J residue 1721 GLU Chi-restraints excluded: chain J residue 1730 MET Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1841 VAL Chi-restraints excluded: chain J residue 1866 ILE Chi-restraints excluded: chain J residue 1939 MET Chi-restraints excluded: chain J residue 1953 HIS Chi-restraints excluded: chain J residue 2135 LEU Chi-restraints excluded: chain J residue 2178 MET Chi-restraints excluded: chain J residue 2358 ILE Chi-restraints excluded: chain J residue 2506 LEU Chi-restraints excluded: chain J residue 2518 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 2959 PHE Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3733 CYS Chi-restraints excluded: chain J residue 3786 CYS Chi-restraints excluded: chain J residue 3798 LEU Chi-restraints excluded: chain J residue 3892 CYS Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4036 VAL Chi-restraints excluded: chain J residue 4097 MET Chi-restraints excluded: chain J residue 4150 LEU Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4201 ASN Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4577 LEU Chi-restraints excluded: chain J residue 4754 ASN Chi-restraints excluded: chain J residue 4853 VAL Chi-restraints excluded: chain J residue 4926 VAL Chi-restraints excluded: chain J residue 4931 ILE Chi-restraints excluded: chain J residue 4967 TYR Chi-restraints excluded: chain K residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 542 optimal weight: 4.9990 chunk 1451 optimal weight: 20.0000 chunk 318 optimal weight: 0.9990 chunk 946 optimal weight: 8.9990 chunk 398 optimal weight: 3.9990 chunk 1613 optimal weight: 3.9990 chunk 1339 optimal weight: 10.0000 chunk 747 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 533 optimal weight: 4.9990 chunk 847 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1571 ASN ** D1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4009 GLN D4054 ASN ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4558 ASN ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS A1254 HIS ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3781 GLN ** A3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4947 GLN B 25 HIS B 70 GLN ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3837 GLN G4020 GLN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 GLN ** J 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 848 HIS ** J1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1719 HIS ** J2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J2349 ASN ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 116571 Z= 0.290 Angle : 0.579 11.008 159543 Z= 0.302 Chirality : 0.039 0.164 19149 Planarity : 0.004 0.071 20607 Dihedral : 4.907 74.087 17677 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.41 % Favored : 97.58 % Rotamer: Outliers : 2.56 % Allowed : 17.89 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.97 (0.07), residues: 16359 helix: 1.79 (0.05), residues: 9028 sheet: -1.13 (0.13), residues: 1447 loop : -0.66 (0.08), residues: 5884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A4716 HIS 0.011 0.001 HIS A2673 PHE 0.029 0.002 PHE A4093 TYR 0.050 0.002 TYR D3968 ARG 0.006 0.000 ARG G5017 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 736 time to evaluate : 9.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 341 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: D 541 SER cc_start: 0.7808 (m) cc_final: 0.7444 (p) REVERT: D 1494 MET cc_start: 0.8190 (mtp) cc_final: 0.7965 (mtp) REVERT: D 2198 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8409 (mmm) REVERT: D 2546 MET cc_start: 0.8546 (tpt) cc_final: 0.8268 (tpp) REVERT: D 3673 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7792 (ttm) REVERT: D 3782 MET cc_start: 0.8525 (ttm) cc_final: 0.8061 (ttm) REVERT: D 3836 MET cc_start: 0.8399 (ttm) cc_final: 0.8170 (ttt) REVERT: D 3899 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8679 (t80) REVERT: D 3943 ILE cc_start: 0.7492 (tp) cc_final: 0.7213 (tp) REVERT: D 3999 MET cc_start: 0.8293 (ptt) cc_final: 0.7934 (ptt) REVERT: D 4047 MET cc_start: 0.8906 (tmm) cc_final: 0.8459 (tmm) REVERT: D 4064 MET cc_start: 0.7986 (mtm) cc_final: 0.7746 (mmm) REVERT: D 4874 MET cc_start: 0.8291 (mmp) cc_final: 0.8048 (mmp) REVERT: E 40 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7805 (tpp-160) REVERT: A 334 MET cc_start: 0.7863 (mmm) cc_final: 0.7620 (mmm) REVERT: A 2618 MET cc_start: 0.8514 (mmt) cc_final: 0.8125 (mmt) REVERT: A 3673 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7707 (ttm) REVERT: A 3820 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8791 (tt) REVERT: A 3899 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.9052 (m-80) REVERT: A 4716 TRP cc_start: 0.8441 (p-90) cc_final: 0.7940 (p-90) REVERT: B 25 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8132 (m-70) REVERT: G 334 MET cc_start: 0.7489 (tpp) cc_final: 0.7285 (tpp) REVERT: G 403 MET cc_start: 0.9156 (mmt) cc_final: 0.8783 (mmt) REVERT: G 540 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8963 (t80) REVERT: G 667 MET cc_start: 0.7427 (tpp) cc_final: 0.6992 (tpp) REVERT: G 1286 MET cc_start: 0.8172 (mmm) cc_final: 0.7822 (tpt) REVERT: G 1636 MET cc_start: 0.8445 (ppp) cc_final: 0.8027 (ppp) REVERT: G 3652 MET cc_start: 0.8851 (mpp) cc_final: 0.8408 (mpp) REVERT: G 3951 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8474 (t80) REVERT: G 3955 MET cc_start: 0.8883 (tpp) cc_final: 0.8415 (mpp) REVERT: G 3999 MET cc_start: 0.9301 (tpp) cc_final: 0.9072 (tpp) REVERT: G 4887 MET cc_start: 0.8700 (mtp) cc_final: 0.8402 (ttm) REVERT: J 181 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7168 (p-80) REVERT: J 540 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: J 1100 MET cc_start: 0.6750 (mmm) cc_final: 0.4863 (ptt) REVERT: J 1494 MET cc_start: 0.7241 (mtm) cc_final: 0.6679 (mtm) REVERT: J 3673 MET cc_start: 0.8133 (tmm) cc_final: 0.7793 (tmm) REVERT: J 4097 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8623 (mtm) REVERT: J 4954 MET cc_start: 0.7382 (tmm) cc_final: 0.7016 (tmm) REVERT: J 4967 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7471 (t80) REVERT: J 4993 MET cc_start: 0.7572 (ttp) cc_final: 0.7062 (tmm) REVERT: L 1 MET cc_start: 0.7044 (ttt) cc_final: 0.6788 (ttt) outliers start: 229 outliers final: 132 residues processed: 920 average time/residue: 0.8521 time to fit residues: 1443.9635 Evaluate side-chains 863 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 716 time to evaluate : 9.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1283 LEU Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1617 THR Chi-restraints excluded: chain D residue 1736 VAL Chi-restraints excluded: chain D residue 1767 VAL Chi-restraints excluded: chain D residue 1841 VAL Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2198 MET Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2581 SER Chi-restraints excluded: chain D residue 3646 THR Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 3897 ASN Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 4010 ILE Chi-restraints excluded: chain D residue 4019 LEU Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4914 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2120 MET Chi-restraints excluded: chain A residue 2290 LEU Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2558 VAL Chi-restraints excluded: chain A residue 3639 THR Chi-restraints excluded: chain A residue 3673 MET Chi-restraints excluded: chain A residue 3793 MET Chi-restraints excluded: chain A residue 3820 LEU Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 3929 SER Chi-restraints excluded: chain A residue 4081 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4741 LEU Chi-restraints excluded: chain A residue 4827 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4985 LEU Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 657 THR Chi-restraints excluded: chain G residue 663 TYR Chi-restraints excluded: chain G residue 716 PHE Chi-restraints excluded: chain G residue 1149 VAL Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1466 LEU Chi-restraints excluded: chain G residue 1520 VAL Chi-restraints excluded: chain G residue 1658 ASP Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1939 MET Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2275 VAL Chi-restraints excluded: chain G residue 2354 VAL Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3656 SER Chi-restraints excluded: chain G residue 3675 ASP Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3899 PHE Chi-restraints excluded: chain G residue 3951 PHE Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4150 LEU Chi-restraints excluded: chain G residue 4223 ASN Chi-restraints excluded: chain G residue 4554 TYR Chi-restraints excluded: chain G residue 4571 PHE Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4936 ILE Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 181 HIS Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 540 PHE Chi-restraints excluded: chain J residue 607 CYS Chi-restraints excluded: chain J residue 1083 VAL Chi-restraints excluded: chain J residue 1437 VAL Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1519 LEU Chi-restraints excluded: chain J residue 1679 ASN Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1953 HIS Chi-restraints excluded: chain J residue 2135 LEU Chi-restraints excluded: chain J residue 2178 MET Chi-restraints excluded: chain J residue 2358 ILE Chi-restraints excluded: chain J residue 2506 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3798 LEU Chi-restraints excluded: chain J residue 3892 CYS Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4097 MET Chi-restraints excluded: chain J residue 4150 LEU Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4577 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4754 ASN Chi-restraints excluded: chain J residue 4931 ILE Chi-restraints excluded: chain J residue 4967 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 1555 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 919 optimal weight: 50.0000 chunk 1178 optimal weight: 4.9990 chunk 913 optimal weight: 9.9990 chunk 1358 optimal weight: 0.0470 chunk 901 optimal weight: 0.8980 chunk 1607 optimal weight: 10.0000 chunk 1006 optimal weight: 2.9990 chunk 980 optimal weight: 1.9990 chunk 742 optimal weight: 8.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 HIS D1563 GLN ** D1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2673 HIS ** A3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1760 HIS ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3900 GLN J3994 HIS K 87 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 116571 Z= 0.178 Angle : 0.525 15.545 159543 Z= 0.269 Chirality : 0.037 0.206 19149 Planarity : 0.003 0.071 20607 Dihedral : 4.490 72.915 17677 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.27 % Allowed : 18.53 % Favored : 79.20 % Cbeta Deviations : 0.00 % 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: 1.52 (0.07), residues: 16359 helix: 2.25 (0.05), residues: 9013 sheet: -0.92 (0.14), residues: 1463 loop : -0.42 (0.08), residues: 5883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A4716 HIS 0.047 0.001 HIS B 25 PHE 0.032 0.001 PHE A4093 TYR 0.059 0.001 TYR A3968 ARG 0.005 0.000 ARG G5017 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 756 time to evaluate : 9.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 341 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: D 578 ILE cc_start: 0.8940 (mm) cc_final: 0.8705 (mm) REVERT: D 1494 MET cc_start: 0.8076 (mtp) cc_final: 0.7847 (mtp) REVERT: D 1573 MET cc_start: 0.8389 (tpp) cc_final: 0.8014 (tpt) REVERT: D 2198 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8378 (mmm) REVERT: D 3673 MET cc_start: 0.8264 (mtm) cc_final: 0.7751 (ttm) REVERT: D 3899 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8662 (t80) REVERT: D 3900 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8290 (mp10) REVERT: D 3962 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: D 4047 MET cc_start: 0.8869 (tmm) cc_final: 0.8423 (tmm) REVERT: D 4064 MET cc_start: 0.7965 (mtm) cc_final: 0.7693 (mmm) REVERT: D 4567 LEU cc_start: 0.9409 (tp) cc_final: 0.9193 (tp) REVERT: D 4947 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: E 40 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7820 (tpp-160) REVERT: A 334 MET cc_start: 0.7807 (mmm) cc_final: 0.7461 (mmm) REVERT: A 1730 MET cc_start: 0.8745 (mmt) cc_final: 0.8457 (mmp) REVERT: A 2502 MET cc_start: 0.8817 (mmm) cc_final: 0.8571 (mmm) REVERT: A 2618 MET cc_start: 0.8524 (mmt) cc_final: 0.8125 (mmt) REVERT: A 3820 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8736 (tt) REVERT: A 3899 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.9007 (m-80) REVERT: A 4639 MET cc_start: 0.8504 (mmp) cc_final: 0.8063 (mmp) REVERT: A 4716 TRP cc_start: 0.8405 (p-90) cc_final: 0.8073 (p-90) REVERT: A 4989 MET cc_start: 0.8203 (tmm) cc_final: 0.7792 (tmt) REVERT: B 25 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8849 (m170) REVERT: G 334 MET cc_start: 0.7658 (tpp) cc_final: 0.7404 (tpp) REVERT: G 667 MET cc_start: 0.7580 (tpp) cc_final: 0.7252 (tpp) REVERT: G 1286 MET cc_start: 0.8148 (mmm) cc_final: 0.7376 (tpt) REVERT: G 1494 MET cc_start: 0.8461 (mtp) cc_final: 0.7937 (mtp) REVERT: G 1636 MET cc_start: 0.8395 (ppp) cc_final: 0.8004 (ppp) REVERT: G 1716 ILE cc_start: 0.9614 (OUTLIER) cc_final: 0.9376 (tt) REVERT: G 3652 MET cc_start: 0.8846 (mpp) cc_final: 0.8372 (mpp) REVERT: G 3820 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9083 (tt) REVERT: G 3951 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8180 (t80) REVERT: G 3955 MET cc_start: 0.8907 (tpp) cc_final: 0.8378 (mpp) REVERT: G 4796 MET cc_start: 0.8780 (tpp) cc_final: 0.8520 (tpp) REVERT: J 180 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8764 (tp) REVERT: J 540 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7531 (m-10) REVERT: J 1100 MET cc_start: 0.6852 (mmm) cc_final: 0.4990 (ptt) REVERT: J 1494 MET cc_start: 0.7228 (mtm) cc_final: 0.6757 (mtp) REVERT: J 3673 MET cc_start: 0.8026 (tmm) cc_final: 0.7716 (tmm) REVERT: J 4097 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8597 (mtm) REVERT: J 4954 MET cc_start: 0.7509 (tmm) cc_final: 0.7118 (tmm) REVERT: J 4967 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7629 (t80) REVERT: J 4993 MET cc_start: 0.7484 (ttp) cc_final: 0.7011 (tmm) REVERT: K 43 ASN cc_start: 0.8652 (m-40) cc_final: 0.8342 (m-40) REVERT: L 1 MET cc_start: 0.7122 (ttt) cc_final: 0.6920 (ttt) outliers start: 203 outliers final: 123 residues processed: 918 average time/residue: 0.8551 time to fit residues: 1439.3257 Evaluate side-chains 875 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 735 time to evaluate : 9.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 506 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1283 LEU Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1554 VAL Chi-restraints excluded: chain D residue 1736 VAL Chi-restraints excluded: chain D residue 1767 VAL Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2198 MET Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2581 SER Chi-restraints excluded: chain D residue 3646 THR Chi-restraints excluded: chain D residue 3897 ASN Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3900 GLN Chi-restraints excluded: chain D residue 3907 THR Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3962 PHE Chi-restraints excluded: chain D residue 4010 ILE Chi-restraints excluded: chain D residue 4019 LEU Chi-restraints excluded: chain D residue 4947 GLN Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2346 VAL Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2558 VAL Chi-restraints excluded: chain A residue 3639 THR Chi-restraints excluded: chain A residue 3820 LEU Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 4081 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 218 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 663 TYR Chi-restraints excluded: chain G residue 716 PHE Chi-restraints excluded: chain G residue 1149 VAL Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1466 LEU Chi-restraints excluded: chain G residue 1716 ILE Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1760 HIS Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2354 VAL Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3820 LEU Chi-restraints excluded: chain G residue 3899 PHE Chi-restraints excluded: chain G residue 3951 PHE Chi-restraints excluded: chain G residue 4029 SER Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4150 LEU Chi-restraints excluded: chain G residue 4223 ASN Chi-restraints excluded: chain G residue 4554 TYR Chi-restraints excluded: chain G residue 4571 PHE Chi-restraints excluded: chain G residue 4785 THR Chi-restraints excluded: chain G residue 4936 ILE Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 540 PHE Chi-restraints excluded: chain J residue 574 VAL Chi-restraints excluded: chain J residue 607 CYS Chi-restraints excluded: chain J residue 764 VAL Chi-restraints excluded: chain J residue 1083 VAL Chi-restraints excluded: chain J residue 1437 VAL Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1519 LEU Chi-restraints excluded: chain J residue 1561 VAL Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1953 HIS Chi-restraints excluded: chain J residue 2135 LEU Chi-restraints excluded: chain J residue 2302 LEU Chi-restraints excluded: chain J residue 2440 MET Chi-restraints excluded: chain J residue 2506 LEU Chi-restraints excluded: chain J residue 2518 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3892 CYS Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4036 VAL Chi-restraints excluded: chain J residue 4097 MET Chi-restraints excluded: chain J residue 4150 LEU Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4754 ASN Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4931 ILE Chi-restraints excluded: chain J residue 4967 TYR Chi-restraints excluded: chain K residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 994 optimal weight: 7.9990 chunk 642 optimal weight: 20.0000 chunk 960 optimal weight: 10.0000 chunk 484 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 1022 optimal weight: 0.9990 chunk 1095 optimal weight: 8.9990 chunk 794 optimal weight: 0.0870 chunk 149 optimal weight: 1.9990 chunk 1263 optimal weight: 5.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1563 GLN D1760 HIS ** D1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2260 ASN ** G4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 HIS J1598 GLN ** J2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 116571 Z= 0.217 Angle : 0.535 16.015 159543 Z= 0.271 Chirality : 0.037 0.187 19149 Planarity : 0.003 0.070 20607 Dihedral : 4.375 73.080 17677 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.43 % Favored : 97.56 % Rotamer: Outliers : 2.26 % Allowed : 18.83 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.07), residues: 16359 helix: 2.34 (0.05), residues: 9023 sheet: -0.89 (0.14), residues: 1464 loop : -0.37 (0.08), residues: 5872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D2680 HIS 0.012 0.001 HIS G1760 PHE 0.034 0.001 PHE A4093 TYR 0.043 0.001 TYR D3968 ARG 0.005 0.000 ARG G5017 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 745 time to evaluate : 9.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 341 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: D 1494 MET cc_start: 0.8082 (mtp) cc_final: 0.7791 (mtp) REVERT: D 1573 MET cc_start: 0.8421 (tpp) cc_final: 0.8174 (tpt) REVERT: D 2198 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8404 (mmm) REVERT: D 3673 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7739 (ttm) REVERT: D 3899 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8606 (t80) REVERT: D 3900 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: D 3943 ILE cc_start: 0.7463 (tp) cc_final: 0.7154 (tp) REVERT: D 3962 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: D 4047 MET cc_start: 0.8872 (tmm) cc_final: 0.8423 (tmm) REVERT: D 4064 MET cc_start: 0.8012 (mtm) cc_final: 0.7739 (mmm) REVERT: D 4231 MET cc_start: 0.8127 (mmm) cc_final: 0.7820 (mtp) REVERT: D 4567 LEU cc_start: 0.9466 (tp) cc_final: 0.9218 (tp) REVERT: D 4874 MET cc_start: 0.7974 (mmp) cc_final: 0.7571 (mmp) REVERT: D 4947 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: E 40 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7847 (tpp-160) REVERT: A 113 HIS cc_start: 0.8833 (OUTLIER) cc_final: 0.8426 (t70) REVERT: A 334 MET cc_start: 0.7829 (mmm) cc_final: 0.7512 (mmm) REVERT: A 1636 MET cc_start: 0.8099 (ttp) cc_final: 0.7754 (ppp) REVERT: A 1730 MET cc_start: 0.8778 (mmt) cc_final: 0.8451 (mmp) REVERT: A 2250 MET cc_start: 0.8647 (tpt) cc_final: 0.8281 (tpt) REVERT: A 3758 MET cc_start: 0.8008 (tpp) cc_final: 0.7453 (tpp) REVERT: A 3820 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8762 (tt) REVERT: A 3899 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.9034 (m-80) REVERT: A 4716 TRP cc_start: 0.8409 (p-90) cc_final: 0.8081 (p-90) REVERT: A 4887 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8137 (mpp) REVERT: G 334 MET cc_start: 0.7707 (tpp) cc_final: 0.7434 (tpp) REVERT: G 403 MET cc_start: 0.9053 (mmm) cc_final: 0.8646 (tpp) REVERT: G 667 MET cc_start: 0.7565 (tpp) cc_final: 0.7242 (tpp) REVERT: G 1286 MET cc_start: 0.8188 (mmm) cc_final: 0.7842 (tpt) REVERT: G 1494 MET cc_start: 0.8530 (mtp) cc_final: 0.7987 (mtp) REVERT: G 1636 MET cc_start: 0.8405 (ppp) cc_final: 0.7986 (ppp) REVERT: G 1716 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9378 (tt) REVERT: G 3652 MET cc_start: 0.8870 (mpp) cc_final: 0.8390 (mpp) REVERT: G 3820 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9068 (tt) REVERT: G 3951 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.7981 (t80) REVERT: G 3955 MET cc_start: 0.8926 (tpp) cc_final: 0.8388 (mpp) REVERT: G 4031 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8610 (mm) REVERT: G 4883 TYR cc_start: 0.9066 (t80) cc_final: 0.8805 (t80) REVERT: J 180 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8759 (tp) REVERT: J 540 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7521 (m-10) REVERT: J 1100 MET cc_start: 0.7073 (mmm) cc_final: 0.5147 (ptt) REVERT: J 1494 MET cc_start: 0.7262 (mtm) cc_final: 0.6832 (mtp) REVERT: J 3673 MET cc_start: 0.8097 (tmm) cc_final: 0.7776 (tmm) REVERT: J 4097 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8561 (mtm) REVERT: J 4954 MET cc_start: 0.7517 (tmm) cc_final: 0.7087 (tmm) REVERT: J 4967 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7600 (t80) REVERT: J 4993 MET cc_start: 0.7479 (ttp) cc_final: 0.7002 (tmm) REVERT: K 43 ASN cc_start: 0.8642 (m-40) cc_final: 0.8421 (m-40) REVERT: L 1 MET cc_start: 0.7157 (ttt) cc_final: 0.6924 (ttt) outliers start: 202 outliers final: 148 residues processed: 907 average time/residue: 0.9266 time to fit residues: 1543.1450 Evaluate side-chains 900 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 732 time to evaluate : 9.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 506 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1554 VAL Chi-restraints excluded: chain D residue 1617 THR Chi-restraints excluded: chain D residue 1736 VAL Chi-restraints excluded: chain D residue 1760 HIS Chi-restraints excluded: chain D residue 1767 VAL Chi-restraints excluded: chain D residue 1841 VAL Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2198 MET Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2581 SER Chi-restraints excluded: chain D residue 3646 THR Chi-restraints excluded: chain D residue 3654 LEU Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 3897 ASN Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3900 GLN Chi-restraints excluded: chain D residue 3907 THR Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3962 PHE Chi-restraints excluded: chain D residue 4010 ILE Chi-restraints excluded: chain D residue 4019 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4801 LEU Chi-restraints excluded: chain D residue 4914 VAL Chi-restraints excluded: chain D residue 4947 GLN Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2120 MET Chi-restraints excluded: chain A residue 2346 VAL Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2558 VAL Chi-restraints excluded: chain A residue 2673 HIS Chi-restraints excluded: chain A residue 3639 THR Chi-restraints excluded: chain A residue 3820 LEU Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 4081 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4887 MET Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 5013 MET Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 218 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 663 TYR Chi-restraints excluded: chain G residue 716 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 1149 VAL Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1466 LEU Chi-restraints excluded: chain G residue 1520 VAL Chi-restraints excluded: chain G residue 1573 MET Chi-restraints excluded: chain G residue 1716 ILE Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2273 LEU Chi-restraints excluded: chain G residue 2354 VAL Chi-restraints excluded: chain G residue 2460 LEU Chi-restraints excluded: chain G residue 2577 ILE Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3644 LEU Chi-restraints excluded: chain G residue 3733 CYS Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3803 SER Chi-restraints excluded: chain G residue 3820 LEU Chi-restraints excluded: chain G residue 3899 PHE Chi-restraints excluded: chain G residue 3951 PHE Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4150 LEU Chi-restraints excluded: chain G residue 4554 TYR Chi-restraints excluded: chain G residue 4571 PHE Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4785 THR Chi-restraints excluded: chain G residue 4936 ILE Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 540 PHE Chi-restraints excluded: chain J residue 574 VAL Chi-restraints excluded: chain J residue 607 CYS Chi-restraints excluded: chain J residue 1083 VAL Chi-restraints excluded: chain J residue 1437 VAL Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1519 LEU Chi-restraints excluded: chain J residue 1561 VAL Chi-restraints excluded: chain J residue 1581 LEU Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1953 HIS Chi-restraints excluded: chain J residue 2135 LEU Chi-restraints excluded: chain J residue 2168 VAL Chi-restraints excluded: chain J residue 2275 VAL Chi-restraints excluded: chain J residue 2302 LEU Chi-restraints excluded: chain J residue 2440 MET Chi-restraints excluded: chain J residue 2456 ILE Chi-restraints excluded: chain J residue 2506 LEU Chi-restraints excluded: chain J residue 2518 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3892 CYS Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4097 MET Chi-restraints excluded: chain J residue 4150 LEU Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4754 ASN Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4931 ILE Chi-restraints excluded: chain J residue 4967 TYR Chi-restraints excluded: chain K residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 1462 optimal weight: 30.0000 chunk 1540 optimal weight: 0.9990 chunk 1405 optimal weight: 6.9990 chunk 1498 optimal weight: 50.0000 chunk 1539 optimal weight: 20.0000 chunk 901 optimal weight: 0.3980 chunk 652 optimal weight: 50.0000 chunk 1176 optimal weight: 3.9990 chunk 459 optimal weight: 5.9990 chunk 1353 optimal weight: 9.9990 chunk 1416 optimal weight: 50.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1760 HIS ** D1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4020 GLN B 25 HIS B 70 GLN ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 HIS ** J2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 116571 Z= 0.289 Angle : 0.572 14.818 159543 Z= 0.290 Chirality : 0.038 0.208 19149 Planarity : 0.004 0.069 20607 Dihedral : 4.406 73.209 17677 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.01 % Favored : 96.98 % Rotamer: Outliers : 2.33 % Allowed : 19.19 % Favored : 78.49 % Cbeta Deviations : 0.00 % 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: 1.59 (0.07), residues: 16359 helix: 2.32 (0.05), residues: 9036 sheet: -0.93 (0.14), residues: 1466 loop : -0.39 (0.08), residues: 5857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D2680 HIS 0.016 0.001 HIS D1760 PHE 0.032 0.001 PHE A4093 TYR 0.040 0.001 TYR D3968 ARG 0.004 0.000 ARG G5017 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 727 time to evaluate : 9.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1494 MET cc_start: 0.8105 (mtp) cc_final: 0.7880 (mtp) REVERT: D 2178 MET cc_start: 0.8204 (tpp) cc_final: 0.7789 (tpp) REVERT: D 2198 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8491 (mmm) REVERT: D 2211 MET cc_start: 0.7823 (tmm) cc_final: 0.7477 (tmm) REVERT: D 2546 MET cc_start: 0.8476 (tpt) cc_final: 0.8181 (tpp) REVERT: D 3673 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7835 (ttm) REVERT: D 3875 MET cc_start: 0.7290 (mmp) cc_final: 0.7055 (mmp) REVERT: D 3899 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8675 (t80) REVERT: D 3900 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: D 3943 ILE cc_start: 0.7506 (tp) cc_final: 0.7204 (tp) REVERT: D 3962 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: D 4047 MET cc_start: 0.8885 (tmm) cc_final: 0.8429 (tmm) REVERT: D 4064 MET cc_start: 0.8016 (mtm) cc_final: 0.7750 (mmm) REVERT: D 4947 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: E 40 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7848 (tpp-160) REVERT: A 113 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8447 (t70) REVERT: A 334 MET cc_start: 0.7851 (mmm) cc_final: 0.7525 (mmm) REVERT: A 1636 MET cc_start: 0.8078 (ttp) cc_final: 0.7714 (ppp) REVERT: A 2250 MET cc_start: 0.8668 (tpt) cc_final: 0.8303 (tpt) REVERT: A 2655 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8643 (m-10) REVERT: A 3820 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8779 (tt) REVERT: A 3899 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.9092 (m-80) REVERT: A 4639 MET cc_start: 0.8547 (mmp) cc_final: 0.8132 (mmp) REVERT: A 4716 TRP cc_start: 0.8519 (p-90) cc_final: 0.8043 (p-90) REVERT: A 4887 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8165 (mpp) REVERT: A 4993 MET cc_start: 0.7659 (ptm) cc_final: 0.7254 (ptm) REVERT: B 25 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.7878 (m-70) REVERT: G 334 MET cc_start: 0.7739 (tpp) cc_final: 0.7462 (tpp) REVERT: G 403 MET cc_start: 0.9063 (mmm) cc_final: 0.8636 (tpp) REVERT: G 540 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8965 (t80) REVERT: G 1286 MET cc_start: 0.8183 (mmm) cc_final: 0.7823 (tpt) REVERT: G 1494 MET cc_start: 0.8550 (mtp) cc_final: 0.8008 (mtp) REVERT: G 1716 ILE cc_start: 0.9612 (OUTLIER) cc_final: 0.9389 (tt) REVERT: G 1929 MET cc_start: 0.8389 (ttm) cc_final: 0.8136 (ttt) REVERT: G 3652 MET cc_start: 0.8878 (mpp) cc_final: 0.8409 (mpp) REVERT: G 3820 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9064 (tt) REVERT: G 3951 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8074 (t80) REVERT: G 3955 MET cc_start: 0.8919 (tpp) cc_final: 0.8376 (mpp) REVERT: G 4031 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8770 (mm) REVERT: J 180 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8789 (tp) REVERT: J 181 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7291 (p-80) REVERT: J 403 MET cc_start: 0.7995 (mmm) cc_final: 0.7732 (mmm) REVERT: J 540 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7562 (m-10) REVERT: J 1100 MET cc_start: 0.7218 (mmm) cc_final: 0.5235 (ptt) REVERT: J 1494 MET cc_start: 0.7315 (mtm) cc_final: 0.6887 (mtp) REVERT: J 3673 MET cc_start: 0.8160 (tmm) cc_final: 0.7842 (tmm) REVERT: J 4097 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8567 (mtm) REVERT: J 4954 MET cc_start: 0.7449 (tmm) cc_final: 0.6819 (tmm) REVERT: J 4967 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7625 (t80) REVERT: J 4993 MET cc_start: 0.7500 (ttp) cc_final: 0.7012 (tmm) REVERT: K 43 ASN cc_start: 0.8678 (m-40) cc_final: 0.8366 (m-40) outliers start: 208 outliers final: 159 residues processed: 893 average time/residue: 0.8476 time to fit residues: 1391.9126 Evaluate side-chains 905 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 723 time to evaluate : 9.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 506 TYR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1554 VAL Chi-restraints excluded: chain D residue 1617 THR Chi-restraints excluded: chain D residue 1648 MET Chi-restraints excluded: chain D residue 1736 VAL Chi-restraints excluded: chain D residue 1760 HIS Chi-restraints excluded: chain D residue 1767 VAL Chi-restraints excluded: chain D residue 1841 VAL Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2198 MET Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2581 SER Chi-restraints excluded: chain D residue 3646 THR Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 3897 ASN Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3900 GLN Chi-restraints excluded: chain D residue 3907 THR Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3962 PHE Chi-restraints excluded: chain D residue 4010 ILE Chi-restraints excluded: chain D residue 4017 LEU Chi-restraints excluded: chain D residue 4019 LEU Chi-restraints excluded: chain D residue 4801 LEU Chi-restraints excluded: chain D residue 4947 GLN Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 1085 SER Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1434 TYR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1839 VAL Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2346 VAL Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2522 LEU Chi-restraints excluded: chain A residue 2558 VAL Chi-restraints excluded: chain A residue 2655 TYR Chi-restraints excluded: chain A residue 2673 HIS Chi-restraints excluded: chain A residue 3639 THR Chi-restraints excluded: chain A residue 3820 LEU Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 4081 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4657 CYS Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4887 MET Chi-restraints excluded: chain A residue 4917 ASP Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 5013 MET Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 218 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 663 TYR Chi-restraints excluded: chain G residue 716 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 1149 VAL Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1466 LEU Chi-restraints excluded: chain G residue 1520 VAL Chi-restraints excluded: chain G residue 1716 ILE Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2273 LEU Chi-restraints excluded: chain G residue 2354 VAL Chi-restraints excluded: chain G residue 2460 LEU Chi-restraints excluded: chain G residue 2577 ILE Chi-restraints excluded: chain G residue 2583 LEU Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3644 LEU Chi-restraints excluded: chain G residue 3733 CYS Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3803 SER Chi-restraints excluded: chain G residue 3820 LEU Chi-restraints excluded: chain G residue 3899 PHE Chi-restraints excluded: chain G residue 3951 PHE Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4150 LEU Chi-restraints excluded: chain G residue 4184 MET Chi-restraints excluded: chain G residue 4223 ASN Chi-restraints excluded: chain G residue 4245 MET Chi-restraints excluded: chain G residue 4554 TYR Chi-restraints excluded: chain G residue 4571 PHE Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4785 THR Chi-restraints excluded: chain G residue 4897 ILE Chi-restraints excluded: chain G residue 4936 ILE Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 181 HIS Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 540 PHE Chi-restraints excluded: chain J residue 574 VAL Chi-restraints excluded: chain J residue 607 CYS Chi-restraints excluded: chain J residue 1083 VAL Chi-restraints excluded: chain J residue 1437 VAL Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1519 LEU Chi-restraints excluded: chain J residue 1561 VAL Chi-restraints excluded: chain J residue 1581 LEU Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1841 VAL Chi-restraints excluded: chain J residue 1953 HIS Chi-restraints excluded: chain J residue 2135 LEU Chi-restraints excluded: chain J residue 2168 VAL Chi-restraints excluded: chain J residue 2178 MET Chi-restraints excluded: chain J residue 2275 VAL Chi-restraints excluded: chain J residue 2302 LEU Chi-restraints excluded: chain J residue 2440 MET Chi-restraints excluded: chain J residue 2456 ILE Chi-restraints excluded: chain J residue 2506 LEU Chi-restraints excluded: chain J residue 2518 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3892 CYS Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4097 MET Chi-restraints excluded: chain J residue 4150 LEU Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4754 ASN Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4931 ILE Chi-restraints excluded: chain J residue 4967 TYR Chi-restraints excluded: chain K residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 1492 optimal weight: 50.0000 chunk 983 optimal weight: 0.3980 chunk 1584 optimal weight: 9.9990 chunk 966 optimal weight: 10.0000 chunk 751 optimal weight: 10.0000 chunk 1101 optimal weight: 10.0000 chunk 1661 optimal weight: 6.9990 chunk 1529 optimal weight: 20.0000 chunk 1323 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 1022 optimal weight: 7.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1571 ASN ** D1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS B 25 HIS B 70 GLN ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1760 HIS ** G2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 116571 Z= 0.392 Angle : 0.630 13.894 159543 Z= 0.321 Chirality : 0.039 0.226 19149 Planarity : 0.004 0.068 20607 Dihedral : 4.552 73.706 17677 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 2.38 % Allowed : 19.23 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.07), residues: 16359 helix: 2.18 (0.05), residues: 9039 sheet: -1.04 (0.13), residues: 1469 loop : -0.51 (0.08), residues: 5851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1143 HIS 0.012 0.001 HIS E 25 PHE 0.033 0.002 PHE A4093 TYR 0.050 0.002 TYR A3968 ARG 0.004 0.000 ARG A 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32718 Ramachandran restraints generated. 16359 Oldfield, 0 Emsley, 16359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 719 time to evaluate : 8.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1100 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8022 (mmm) REVERT: D 1494 MET cc_start: 0.8180 (mtp) cc_final: 0.7955 (mtp) REVERT: D 2198 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8512 (mmm) REVERT: D 2211 MET cc_start: 0.7873 (tmm) cc_final: 0.7538 (tmm) REVERT: D 2546 MET cc_start: 0.8568 (tpt) cc_final: 0.8297 (tpp) REVERT: D 3673 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7868 (ttm) REVERT: D 3875 MET cc_start: 0.7334 (mmp) cc_final: 0.6990 (mmp) REVERT: D 3899 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8643 (t80) REVERT: D 3900 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: D 3943 ILE cc_start: 0.7529 (tp) cc_final: 0.7239 (tp) REVERT: D 3962 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: D 4047 MET cc_start: 0.8897 (tmm) cc_final: 0.8438 (tmm) REVERT: D 4874 MET cc_start: 0.7986 (mmp) cc_final: 0.7643 (mmp) REVERT: D 4947 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: E 40 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7099 (tpp-160) REVERT: A 113 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8422 (t70) REVERT: A 334 MET cc_start: 0.7887 (mmm) cc_final: 0.7560 (mmm) REVERT: A 1636 MET cc_start: 0.8080 (ttp) cc_final: 0.7695 (ppp) REVERT: A 1929 MET cc_start: 0.9104 (pmm) cc_final: 0.8779 (ptp) REVERT: A 2618 MET cc_start: 0.8636 (mmm) cc_final: 0.8390 (mmm) REVERT: A 2655 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8599 (m-10) REVERT: A 3820 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8802 (tt) REVERT: A 3899 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.9077 (m-80) REVERT: A 4716 TRP cc_start: 0.8599 (p-90) cc_final: 0.8003 (p-90) REVERT: A 4887 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8217 (mpp) REVERT: B 25 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.7956 (m-70) REVERT: G 334 MET cc_start: 0.7721 (tpp) cc_final: 0.7424 (tpp) REVERT: G 540 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.9083 (t80) REVERT: G 667 MET cc_start: 0.7470 (mmm) cc_final: 0.7186 (tpp) REVERT: G 1286 MET cc_start: 0.8160 (mmm) cc_final: 0.7785 (tpt) REVERT: G 1601 MET cc_start: 0.8804 (mmm) cc_final: 0.8538 (mmm) REVERT: G 1716 ILE cc_start: 0.9621 (OUTLIER) cc_final: 0.9399 (tt) REVERT: G 1929 MET cc_start: 0.8416 (ttm) cc_final: 0.8166 (ttt) REVERT: G 3652 MET cc_start: 0.8881 (mpp) cc_final: 0.8426 (mpp) REVERT: G 3820 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9088 (tt) REVERT: G 3951 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8125 (t80) REVERT: G 3955 MET cc_start: 0.8945 (tpp) cc_final: 0.8404 (mpp) REVERT: G 4031 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8695 (mm) REVERT: J 180 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8796 (tp) REVERT: J 181 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7298 (p-80) REVERT: J 403 MET cc_start: 0.8016 (mmm) cc_final: 0.7751 (mmm) REVERT: J 540 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: J 1100 MET cc_start: 0.7340 (mmm) cc_final: 0.5230 (ptt) REVERT: J 1494 MET cc_start: 0.7326 (mtm) cc_final: 0.6911 (mtp) REVERT: J 3673 MET cc_start: 0.8180 (tmm) cc_final: 0.7837 (tmm) REVERT: J 4097 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8470 (mtm) REVERT: J 4954 MET cc_start: 0.7408 (tmm) cc_final: 0.7145 (tmm) REVERT: J 4967 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.7613 (t80) REVERT: J 4993 MET cc_start: 0.7527 (ttp) cc_final: 0.7021 (tmm) outliers start: 213 outliers final: 163 residues processed: 889 average time/residue: 0.8633 time to fit residues: 1408.1736 Evaluate side-chains 896 residues out of total 14588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 709 time to evaluate : 9.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 791 PHE Chi-restraints excluded: chain D residue 1100 MET Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1427 ILE Chi-restraints excluded: chain D residue 1437 VAL Chi-restraints excluded: chain D residue 1520 VAL Chi-restraints excluded: chain D residue 1554 VAL Chi-restraints excluded: chain D residue 1617 THR Chi-restraints excluded: chain D residue 1648 MET Chi-restraints excluded: chain D residue 1736 VAL Chi-restraints excluded: chain D residue 1767 VAL Chi-restraints excluded: chain D residue 1841 VAL Chi-restraints excluded: chain D residue 1966 VAL Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2198 MET Chi-restraints excluded: chain D residue 2341 VAL Chi-restraints excluded: chain D residue 2506 LEU Chi-restraints excluded: chain D residue 2581 SER Chi-restraints excluded: chain D residue 3646 THR Chi-restraints excluded: chain D residue 3654 LEU Chi-restraints excluded: chain D residue 3673 MET Chi-restraints excluded: chain D residue 3897 ASN Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3900 GLN Chi-restraints excluded: chain D residue 3907 THR Chi-restraints excluded: chain D residue 3923 LEU Chi-restraints excluded: chain D residue 3962 PHE Chi-restraints excluded: chain D residue 4010 ILE Chi-restraints excluded: chain D residue 4017 LEU Chi-restraints excluded: chain D residue 4019 LEU Chi-restraints excluded: chain D residue 4801 LEU Chi-restraints excluded: chain D residue 4947 GLN Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 1085 SER Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1434 TYR Chi-restraints excluded: chain A residue 1437 VAL Chi-restraints excluded: chain A residue 1736 VAL Chi-restraints excluded: chain A residue 1769 THR Chi-restraints excluded: chain A residue 1839 VAL Chi-restraints excluded: chain A residue 1979 LEU Chi-restraints excluded: chain A residue 2120 MET Chi-restraints excluded: chain A residue 2518 LEU Chi-restraints excluded: chain A residue 2522 LEU Chi-restraints excluded: chain A residue 2558 VAL Chi-restraints excluded: chain A residue 2655 TYR Chi-restraints excluded: chain A residue 2673 HIS Chi-restraints excluded: chain A residue 3639 THR Chi-restraints excluded: chain A residue 3820 LEU Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3912 THR Chi-restraints excluded: chain A residue 3929 SER Chi-restraints excluded: chain A residue 4081 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4657 CYS Chi-restraints excluded: chain A residue 4827 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4887 MET Chi-restraints excluded: chain A residue 4917 ASP Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 5013 MET Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 218 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 540 PHE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain G residue 663 TYR Chi-restraints excluded: chain G residue 716 PHE Chi-restraints excluded: chain G residue 826 ILE Chi-restraints excluded: chain G residue 1149 VAL Chi-restraints excluded: chain G residue 1437 VAL Chi-restraints excluded: chain G residue 1466 LEU Chi-restraints excluded: chain G residue 1520 VAL Chi-restraints excluded: chain G residue 1573 MET Chi-restraints excluded: chain G residue 1716 ILE Chi-restraints excluded: chain G residue 1736 VAL Chi-restraints excluded: chain G residue 1939 MET Chi-restraints excluded: chain G residue 1966 VAL Chi-restraints excluded: chain G residue 2128 TYR Chi-restraints excluded: chain G residue 2273 LEU Chi-restraints excluded: chain G residue 2354 VAL Chi-restraints excluded: chain G residue 2460 LEU Chi-restraints excluded: chain G residue 2577 ILE Chi-restraints excluded: chain G residue 2583 LEU Chi-restraints excluded: chain G residue 2619 LEU Chi-restraints excluded: chain G residue 3015 LEU Chi-restraints excluded: chain G residue 3644 LEU Chi-restraints excluded: chain G residue 3733 CYS Chi-restraints excluded: chain G residue 3764 LEU Chi-restraints excluded: chain G residue 3782 MET Chi-restraints excluded: chain G residue 3803 SER Chi-restraints excluded: chain G residue 3820 LEU Chi-restraints excluded: chain G residue 3899 PHE Chi-restraints excluded: chain G residue 3951 PHE Chi-restraints excluded: chain G residue 4031 LEU Chi-restraints excluded: chain G residue 4150 LEU Chi-restraints excluded: chain G residue 4184 MET Chi-restraints excluded: chain G residue 4223 ASN Chi-restraints excluded: chain G residue 4245 MET Chi-restraints excluded: chain G residue 4554 TYR Chi-restraints excluded: chain G residue 4648 LEU Chi-restraints excluded: chain G residue 4785 THR Chi-restraints excluded: chain G residue 4897 ILE Chi-restraints excluded: chain G residue 4936 ILE Chi-restraints excluded: chain G residue 4992 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 181 HIS Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 308 HIS Chi-restraints excluded: chain J residue 522 LEU Chi-restraints excluded: chain J residue 540 PHE Chi-restraints excluded: chain J residue 574 VAL Chi-restraints excluded: chain J residue 607 CYS Chi-restraints excluded: chain J residue 1083 VAL Chi-restraints excluded: chain J residue 1437 VAL Chi-restraints excluded: chain J residue 1454 THR Chi-restraints excluded: chain J residue 1561 VAL Chi-restraints excluded: chain J residue 1581 LEU Chi-restraints excluded: chain J residue 1767 VAL Chi-restraints excluded: chain J residue 1841 VAL Chi-restraints excluded: chain J residue 1953 HIS Chi-restraints excluded: chain J residue 2135 LEU Chi-restraints excluded: chain J residue 2168 VAL Chi-restraints excluded: chain J residue 2178 MET Chi-restraints excluded: chain J residue 2275 VAL Chi-restraints excluded: chain J residue 2302 LEU Chi-restraints excluded: chain J residue 2506 LEU Chi-restraints excluded: chain J residue 2518 LEU Chi-restraints excluded: chain J residue 2553 TYR Chi-restraints excluded: chain J residue 3696 ASP Chi-restraints excluded: chain J residue 3892 CYS Chi-restraints excluded: chain J residue 3905 THR Chi-restraints excluded: chain J residue 3910 THR Chi-restraints excluded: chain J residue 3911 THR Chi-restraints excluded: chain J residue 4097 MET Chi-restraints excluded: chain J residue 4150 LEU Chi-restraints excluded: chain J residue 4183 ILE Chi-restraints excluded: chain J residue 4245 MET Chi-restraints excluded: chain J residue 4565 LEU Chi-restraints excluded: chain J residue 4580 TYR Chi-restraints excluded: chain J residue 4582 VAL Chi-restraints excluded: chain J residue 4754 ASN Chi-restraints excluded: chain J residue 4820 VAL Chi-restraints excluded: chain J residue 4931 ILE Chi-restraints excluded: chain J residue 4967 TYR Chi-restraints excluded: chain K residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1668 random chunks: chunk 811 optimal weight: 10.0000 chunk 1051 optimal weight: 1.9990 chunk 1409 optimal weight: 0.0040 chunk 405 optimal weight: 5.9990 chunk 1220 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 367 optimal weight: 20.0000 chunk 1325 optimal weight: 8.9990 chunk 554 optimal weight: 0.8980 chunk 1360 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 overall best weight: 3.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1563 GLN D1760 HIS ** D1970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** A1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS B 25 HIS ** G 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3960 GLN ** G4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J3994 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.067209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051103 restraints weight = 607006.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.052295 restraints weight = 302570.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052835 restraints weight = 166511.587| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 116571 Z= 0.259 Angle : 0.569 15.452 159543 Z= 0.287 Chirality : 0.038 0.220 19149 Planarity : 0.004 0.067 20607 Dihedral : 4.435 72.279 17677 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.38 % Allowed : 19.34 % Favored : 78.27 % Cbeta Deviations : 0.00 % 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: 1.56 (0.07), residues: 16359 helix: 2.30 (0.05), residues: 9028 sheet: -0.97 (0.13), residues: 1481 loop : -0.43 (0.08), residues: 5850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 546 HIS 0.018 0.001 HIS B 25 PHE 0.035 0.001 PHE A4093 TYR 0.048 0.001 TYR A3968 ARG 0.004 0.000 ARG G5017 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23690.92 seconds wall clock time: 414 minutes 43.87 seconds (24883.87 seconds total)