Starting phenix.real_space_refine on Tue Mar 19 01:44:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9z_26410/03_2024/7u9z_26410_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9z_26410/03_2024/7u9z_26410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9z_26410/03_2024/7u9z_26410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9z_26410/03_2024/7u9z_26410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9z_26410/03_2024/7u9z_26410_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u9z_26410/03_2024/7u9z_26410_updated.pdb" } resolution = 3.29 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= 0.012 sd= 0.032 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 24 5.49 5 S 936 5.16 5 C 88244 2.51 5 N 23616 2.21 5 O 25860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2793": "NH1" <-> "NH2" Residue "A PHE 2963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3176": "OD1" <-> "OD2" Residue "A TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3848": "OE1" <-> "OE2" Residue "A PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "B TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2793": "NH1" <-> "NH2" Residue "B PHE 2963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3176": "OD1" <-> "OD2" Residue "B TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3848": "OE1" <-> "OE2" Residue "B PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2793": "NH1" <-> "NH2" Residue "C PHE 2963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3176": "OD1" <-> "OD2" Residue "C TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3848": "OE1" <-> "OE2" Residue "C PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2793": "NH1" <-> "NH2" Residue "D PHE 2963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3176": "OD1" <-> "OD2" Residue "D TYR 3184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3848": "OE1" <-> "OE2" Residue "D PHE 4174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.45s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138688 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33779 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4226, 33771 Classifications: {'peptide': 4226} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4069} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4226, 33771 Classifications: {'peptide': 4226} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4069} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34494 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 33779 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4226, 33771 Classifications: {'peptide': 4226} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4069} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4226, 33771 Classifications: {'peptide': 4226} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4069} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34494 Chain: "C" Number of atoms: 33779 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4226, 33771 Classifications: {'peptide': 4226} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4069} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4226, 33771 Classifications: {'peptide': 4226} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4069} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34494 Chain: "D" Number of atoms: 33779 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4226, 33771 Classifications: {'peptide': 4226} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4069} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4226, 33771 Classifications: {'peptide': 4226} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4069} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34494 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'XAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33100 SG CYS A4888 166.059 197.146 125.933 1.00169.30 S ATOM 33125 SG CYS A4891 166.924 194.662 123.137 1.00159.57 S ATOM 70151 SG CYS B4888 196.346 199.530 126.104 1.00177.32 S ATOM 70176 SG CYS B4891 193.882 198.663 123.291 1.00167.90 S ATOM A0316 SG CYS C4888 198.707 169.079 125.711 1.00176.96 S ATOM A031V SG CYS C4891 197.842 171.533 122.888 1.00166.42 S ATOM A0T3H SG CYS D4888 168.478 166.664 125.997 1.00181.87 S ATOM A0T46 SG CYS D4891 170.941 167.510 123.176 1.00178.22 S Time building chain proxies: 99.95, per 1000 atoms: 0.72 Number of scatterers: 138688 At special positions: 0 Unit cell: (366.08, 366.912, 211.328, 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 936 16.00 P 24 15.00 O 25860 8.00 N 23616 7.00 C 88244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 44.27 Conformation dependent library (CDL) restraints added in 34.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 4 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32480 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: 692 helices and 80 sheets defined 58.8% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 43.23 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.676A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.670A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 271 removed outlier: 6.616A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 5.445A pdb=" N THR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.679A pdb=" N HIS A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.589A pdb=" N VAL A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 removed outlier: 3.891A pdb=" N VAL A 517 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.649A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 555 removed outlier: 4.289A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 563 removed outlier: 4.155A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 5.384A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.590A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.631A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 879 through 901 removed outlier: 4.335A pdb=" N GLU A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 946 removed outlier: 3.699A pdb=" N SER A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 962 removed outlier: 5.654A pdb=" N LYS A 962 " --> pdb=" O GLU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 5.126A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.203A pdb=" N ILE A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 982 through 987' Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1040 through 1061 Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.934A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1226 through 1231 removed outlier: 3.583A pdb=" N GLY A1231 " --> pdb=" O PHE A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 3.958A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.885A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.152A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1648' Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.595A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.838A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1723 removed outlier: 4.581A pdb=" N ASN A1723 " --> pdb=" O LEU A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.634A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1803 Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1835 through 1847 Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 4.432A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1951 removed outlier: 4.008A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1968 removed outlier: 5.247A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Proline residue: A1968 - end of helix Processing helix chain 'A' and resid 1969 through 1978 Processing helix chain 'A' and resid 1989 through 2008 Processing helix chain 'A' and resid 2057 through 2073 Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.883A pdb=" N GLY A2094 " --> pdb=" O ARG A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.910A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.526A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 3.743A pdb=" N GLY A2181 " --> pdb=" O ASN A2177 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.599A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2218 removed outlier: 3.714A pdb=" N ASP A2216 " --> pdb=" O LYS A2212 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2219 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 4.060A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2332 through 2337 removed outlier: 3.941A pdb=" N ARG A2336 " --> pdb=" O GLY A2332 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY A2337 " --> pdb=" O PRO A2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2332 through 2337' Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2377 through 2382 removed outlier: 4.721A pdb=" N ILE A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) Processing helix chain 'A' and resid 2383 through 2403 Processing helix chain 'A' and resid 2405 through 2412 Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2438 Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 4.196A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2504 removed outlier: 3.767A pdb=" N ASP A2503 " --> pdb=" O ALA A2499 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 3.716A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 5.550A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 5.290A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 Processing helix chain 'A' and resid 2585 through 2596 Processing helix chain 'A' and resid 2603 through 2618 Processing helix chain 'A' and resid 2634 through 2655 Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2694 through 2699 removed outlier: 4.183A pdb=" N GLU A2698 " --> pdb=" O SER A2694 " (cutoff:3.500A) Processing helix chain 'A' and resid 2717 through 2740 Processing helix chain 'A' and resid 2767 through 2786 Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2834 through 2864 removed outlier: 3.873A pdb=" N GLY A2864 " --> pdb=" O LEU A2860 " (cutoff:3.500A) Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.260A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.808A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2915 through 2920 removed outlier: 6.506A pdb=" N LYS A2919 " --> pdb=" O PRO A2915 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ARG A2920 " --> pdb=" O SER A2916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2915 through 2920' Processing helix chain 'A' and resid 2925 through 2947 removed outlier: 4.240A pdb=" N ASP A2934 " --> pdb=" O ILE A2930 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU A2935 " --> pdb=" O ARG A2931 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA A2936 " --> pdb=" O TYR A2932 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS A2937 " --> pdb=" O VAL A2933 " (cutoff:3.500A) Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.891A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2997 through 3015 removed outlier: 6.086A pdb=" N GLU A3002 " --> pdb=" O ASN A2998 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A3008 " --> pdb=" O VAL A3004 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N CYS A3009 " --> pdb=" O THR A3005 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS A3010 " --> pdb=" O SER A3006 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A3011 " --> pdb=" O LEU A3007 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A3014 " --> pdb=" O LYS A3010 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL A3015 " --> pdb=" O LEU A3011 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3023 removed outlier: 4.225A pdb=" N LEU A3021 " --> pdb=" O HIS A3017 " (cutoff:3.500A) Processing helix chain 'A' and resid 3024 through 3040 removed outlier: 4.357A pdb=" N SER A3028 " --> pdb=" O ASN A3024 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A3040 " --> pdb=" O LEU A3036 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3048 Processing helix chain 'A' and resid 3050 through 3077 removed outlier: 4.262A pdb=" N GLN A3077 " --> pdb=" O GLU A3073 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 4.857A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3117 through 3122 Processing helix chain 'A' and resid 3124 through 3143 Processing helix chain 'A' and resid 3145 through 3150 removed outlier: 3.763A pdb=" N GLU A3149 " --> pdb=" O SER A3145 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3145 through 3150' Processing helix chain 'A' and resid 3151 through 3166 removed outlier: 3.636A pdb=" N GLU A3157 " --> pdb=" O SER A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3172 through 3180 removed outlier: 4.915A pdb=" N ASP A3176 " --> pdb=" O GLU A3172 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS A3177 " --> pdb=" O THR A3173 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS A3178 " --> pdb=" O HIS A3174 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3182 through 3188 Processing helix chain 'A' and resid 3190 through 3196 removed outlier: 4.800A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 removed outlier: 5.085A pdb=" N CYS A3205 " --> pdb=" O VAL A3201 " (cutoff:3.500A) Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3224 removed outlier: 5.455A pdb=" N ALA A3222 " --> pdb=" O ILE A3218 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A3223 " --> pdb=" O VAL A3219 " (cutoff:3.500A) Processing helix chain 'A' and resid 3232 through 3254 removed outlier: 4.653A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix removed outlier: 5.165A pdb=" N GLY A3253 " --> pdb=" O TRP A3249 " (cutoff:3.500A) Proline residue: A3254 - end of helix Processing helix chain 'A' and resid 3260 through 3265 removed outlier: 6.590A pdb=" N CYS A3264 " --> pdb=" O ARG A3260 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N CYS A3265 " --> pdb=" O ALA A3261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3260 through 3265' Processing helix chain 'A' and resid 3270 through 3291 removed outlier: 5.106A pdb=" N ASN A3274 " --> pdb=" O SER A3270 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY A3278 " --> pdb=" O ASN A3274 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP A3291 " --> pdb=" O ASN A3287 " (cutoff:3.500A) Processing helix chain 'A' and resid 3297 through 3307 Proline residue: A3305 - end of helix Processing helix chain 'A' and resid 3311 through 3337 removed outlier: 5.185A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS A3318 " --> pdb=" O LEU A3314 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix Processing helix chain 'A' and resid 3600 through 3606 removed outlier: 6.025A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.961A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3628 Processing helix chain 'A' and resid 3636 through 3647 Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3649 through 3654 Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.789A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.904A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.200A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 removed outlier: 6.042A pdb=" N ARG A3810 " --> pdb=" O ASN A3806 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A3811 " --> pdb=" O ALA A3807 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3848 Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.870A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.571A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3938 Processing helix chain 'A' and resid 3939 through 3962 removed outlier: 3.663A pdb=" N ALA A3943 " --> pdb=" O ARG A3939 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4027 removed outlier: 4.038A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4029 through 4037 removed outlier: 3.777A pdb=" N TYR A4035 " --> pdb=" O THR A4031 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A4036 " --> pdb=" O PHE A4032 " (cutoff:3.500A) Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.070A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 3.849A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.933A pdb=" N ASP A4093 " --> pdb=" O GLU A4089 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY A4095 " --> pdb=" O ALA A4091 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A4098 " --> pdb=" O ILE A4094 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 removed outlier: 3.550A pdb=" N PHE A4118 " --> pdb=" O ARG A4114 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4131 Proline residue: A4131 - end of helix Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4183 through 4207 removed outlier: 4.144A pdb=" N GLU A4187 " --> pdb=" O LYS A4183 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4268 removed outlier: 6.895A pdb=" N LYS A4262 " --> pdb=" O MET A4258 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N SER A4263 " --> pdb=" O LEU A4259 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A4264 " --> pdb=" O SER A4260 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET A4268 " --> pdb=" O LEU A4264 " (cutoff:3.500A) Processing helix chain 'A' and resid 4269 through 4274 Processing helix chain 'A' and resid 4275 through 4310 removed outlier: 5.499A pdb=" N MET A4279 " --> pdb=" O THR A4275 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A4298 " --> pdb=" O LEU A4294 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A4299 " --> pdb=" O LEU A4295 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL A4301 " --> pdb=" O PHE A4297 " (cutoff:3.500A) Processing helix chain 'A' and resid 4483 through 4499 removed outlier: 5.324A pdb=" N TYR A4487 " --> pdb=" O LYS A4483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A4492 " --> pdb=" O GLN A4488 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN A4493 " --> pdb=" O GLN A4489 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR A4494 " --> pdb=" O LYS A4490 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE A4495 " --> pdb=" O LEU A4491 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA A4496 " --> pdb=" O LEU A4492 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 3.658A pdb=" N LEU A4518 " --> pdb=" O ASN A4514 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4569 through 4612 removed outlier: 3.868A pdb=" N ARG A4573 " --> pdb=" O GLU A4569 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR A4590 " --> pdb=" O CYS A4586 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A4591 " --> pdb=" O ILE A4587 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU A4593 " --> pdb=" O GLY A4589 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4636 removed outlier: 4.331A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4658 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4675 through 4684 removed outlier: 4.007A pdb=" N GLU A4684 " --> pdb=" O SER A4680 " (cutoff:3.500A) Processing helix chain 'A' and resid 4695 through 4701 removed outlier: 4.441A pdb=" N ILE A4701 " --> pdb=" O VAL A4697 " (cutoff:3.500A) Processing helix chain 'A' and resid 4702 through 4717 removed outlier: 5.562A pdb=" N ASN A4717 " --> pdb=" O VAL A4713 " (cutoff:3.500A) Processing helix chain 'A' and resid 4718 through 4735 removed outlier: 4.109A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.508A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 3.940A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR A4761 " --> pdb=" O LEU A4757 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 4.349A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 4.093A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.203A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4883 Processing helix chain 'A' and resid 4894 through 4902 removed outlier: 4.116A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A4901 " --> pdb=" O TYR A4897 " (cutoff:3.500A) Proline residue: A4902 - end of helix Processing helix chain 'A' and resid 4903 through 4911 removed outlier: 3.824A pdb=" N LEU A4910 " --> pdb=" O GLU A4906 " (cutoff:3.500A) Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 5.592A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR A1776 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A1777 " --> pdb=" O GLU A1774 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1772 through 1778' Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.676A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.670A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 removed outlier: 6.616A pdb=" N SER B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 removed outlier: 5.445A pdb=" N THR B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 448 through 464 removed outlier: 3.679A pdb=" N HIS B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 508 removed outlier: 3.589A pdb=" N VAL B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.891A pdb=" N VAL B 517 " --> pdb=" O HIS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.649A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 555 removed outlier: 4.289A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 563 removed outlier: 4.156A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 5.383A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.590A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.630A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 879 through 901 removed outlier: 4.335A pdb=" N GLU B 883 " --> pdb=" O GLU B 879 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 946 removed outlier: 3.699A pdb=" N SER B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 962 removed outlier: 5.655A pdb=" N LYS B 962 " --> pdb=" O GLU B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 5.126A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.203A pdb=" N ILE B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 982 through 987' Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1040 through 1061 Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.934A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1226 through 1231 removed outlier: 3.583A pdb=" N GLY B1231 " --> pdb=" O PHE B1227 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 3.958A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.884A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.151A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1640 through 1648' Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.596A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.838A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1723 removed outlier: 4.581A pdb=" N ASN B1723 " --> pdb=" O LEU B1719 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.633A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1803 Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1835 through 1847 Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 4.433A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1951 removed outlier: 4.008A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1968 removed outlier: 5.247A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Proline residue: B1968 - end of helix Processing helix chain 'B' and resid 1969 through 1978 Processing helix chain 'B' and resid 1989 through 2008 Processing helix chain 'B' and resid 2057 through 2073 Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.883A pdb=" N GLY B2094 " --> pdb=" O ARG B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.910A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.526A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 3.742A pdb=" N GLY B2181 " --> pdb=" O ASN B2177 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.599A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2218 removed outlier: 3.713A pdb=" N ASP B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) Processing helix chain 'B' and resid 2219 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 4.061A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B2298 " --> pdb=" O GLU B2294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2332 through 2337 removed outlier: 3.942A pdb=" N ARG B2336 " --> pdb=" O GLY B2332 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLY B2337 " --> pdb=" O PRO B2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2332 through 2337' Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2377 through 2382 removed outlier: 4.721A pdb=" N ILE B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) Processing helix chain 'B' and resid 2383 through 2403 Processing helix chain 'B' and resid 2405 through 2412 Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2438 Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 4.197A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2504 removed outlier: 3.768A pdb=" N ASP B2503 " --> pdb=" O ALA B2499 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 3.717A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 5.550A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 5.291A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 Processing helix chain 'B' and resid 2585 through 2596 Processing helix chain 'B' and resid 2603 through 2618 Processing helix chain 'B' and resid 2634 through 2655 Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2694 through 2699 removed outlier: 4.184A pdb=" N GLU B2698 " --> pdb=" O SER B2694 " (cutoff:3.500A) Processing helix chain 'B' and resid 2717 through 2740 Processing helix chain 'B' and resid 2767 through 2786 Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2834 through 2864 removed outlier: 3.872A pdb=" N GLY B2864 " --> pdb=" O LEU B2860 " (cutoff:3.500A) Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.259A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.807A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2915 through 2920 removed outlier: 6.505A pdb=" N LYS B2919 " --> pdb=" O PRO B2915 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG B2920 " --> pdb=" O SER B2916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2915 through 2920' Processing helix chain 'B' and resid 2925 through 2947 removed outlier: 4.239A pdb=" N ASP B2934 " --> pdb=" O ILE B2930 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU B2935 " --> pdb=" O ARG B2931 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA B2936 " --> pdb=" O TYR B2932 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS B2937 " --> pdb=" O VAL B2933 " (cutoff:3.500A) Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.891A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2997 through 3015 removed outlier: 6.087A pdb=" N GLU B3002 " --> pdb=" O ASN B2998 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B3008 " --> pdb=" O VAL B3004 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N CYS B3009 " --> pdb=" O THR B3005 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS B3010 " --> pdb=" O SER B3006 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B3011 " --> pdb=" O LEU B3007 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B3014 " --> pdb=" O LYS B3010 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL B3015 " --> pdb=" O LEU B3011 " (cutoff:3.500A) Processing helix chain 'B' and resid 3017 through 3023 removed outlier: 4.226A pdb=" N LEU B3021 " --> pdb=" O HIS B3017 " (cutoff:3.500A) Processing helix chain 'B' and resid 3024 through 3040 removed outlier: 4.357A pdb=" N SER B3028 " --> pdb=" O ASN B3024 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU B3040 " --> pdb=" O LEU B3036 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3048 Processing helix chain 'B' and resid 3050 through 3077 removed outlier: 4.262A pdb=" N GLN B3077 " --> pdb=" O GLU B3073 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 4.858A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3117 through 3122 Processing helix chain 'B' and resid 3124 through 3143 Processing helix chain 'B' and resid 3145 through 3150 removed outlier: 3.763A pdb=" N GLU B3149 " --> pdb=" O SER B3145 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3145 through 3150' Processing helix chain 'B' and resid 3151 through 3166 removed outlier: 3.636A pdb=" N GLU B3157 " --> pdb=" O SER B3153 " (cutoff:3.500A) Processing helix chain 'B' and resid 3172 through 3180 removed outlier: 4.915A pdb=" N ASP B3176 " --> pdb=" O GLU B3172 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS B3177 " --> pdb=" O THR B3173 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N HIS B3178 " --> pdb=" O HIS B3174 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) Processing helix chain 'B' and resid 3182 through 3188 Processing helix chain 'B' and resid 3190 through 3196 removed outlier: 4.801A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 removed outlier: 5.084A pdb=" N CYS B3205 " --> pdb=" O VAL B3201 " (cutoff:3.500A) Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3224 removed outlier: 5.456A pdb=" N ALA B3222 " --> pdb=" O ILE B3218 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU B3223 " --> pdb=" O VAL B3219 " (cutoff:3.500A) Processing helix chain 'B' and resid 3232 through 3254 removed outlier: 4.652A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix removed outlier: 5.165A pdb=" N GLY B3253 " --> pdb=" O TRP B3249 " (cutoff:3.500A) Proline residue: B3254 - end of helix Processing helix chain 'B' and resid 3260 through 3265 removed outlier: 6.590A pdb=" N CYS B3264 " --> pdb=" O ARG B3260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N CYS B3265 " --> pdb=" O ALA B3261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3260 through 3265' Processing helix chain 'B' and resid 3270 through 3291 removed outlier: 5.105A pdb=" N ASN B3274 " --> pdb=" O SER B3270 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY B3278 " --> pdb=" O ASN B3274 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP B3291 " --> pdb=" O ASN B3287 " (cutoff:3.500A) Processing helix chain 'B' and resid 3297 through 3307 Proline residue: B3305 - end of helix Processing helix chain 'B' and resid 3311 through 3337 removed outlier: 5.186A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS B3318 " --> pdb=" O LEU B3314 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix Processing helix chain 'B' and resid 3600 through 3606 removed outlier: 6.025A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.960A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3628 Processing helix chain 'B' and resid 3636 through 3647 Proline residue: B3647 - end of helix Processing helix chain 'B' and resid 3649 through 3654 Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.788A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.904A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.199A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 removed outlier: 6.043A pdb=" N ARG B3810 " --> pdb=" O ASN B3806 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B3811 " --> pdb=" O ALA B3807 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3848 Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.870A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.571A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3938 Processing helix chain 'B' and resid 3939 through 3962 removed outlier: 3.662A pdb=" N ALA B3943 " --> pdb=" O ARG B3939 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4027 removed outlier: 4.037A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4029 through 4037 removed outlier: 3.778A pdb=" N TYR B4035 " --> pdb=" O THR B4031 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B4036 " --> pdb=" O PHE B4032 " (cutoff:3.500A) Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.071A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 3.849A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.934A pdb=" N ASP B4093 " --> pdb=" O GLU B4089 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY B4095 " --> pdb=" O ALA B4091 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B4098 " --> pdb=" O ILE B4094 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 removed outlier: 3.550A pdb=" N PHE B4118 " --> pdb=" O ARG B4114 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4131 Proline residue: B4131 - end of helix Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4183 through 4207 removed outlier: 4.144A pdb=" N GLU B4187 " --> pdb=" O LYS B4183 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4268 removed outlier: 6.896A pdb=" N LYS B4262 " --> pdb=" O MET B4258 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER B4263 " --> pdb=" O LEU B4259 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B4264 " --> pdb=" O SER B4260 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B4268 " --> pdb=" O LEU B4264 " (cutoff:3.500A) Processing helix chain 'B' and resid 4269 through 4274 Processing helix chain 'B' and resid 4275 through 4310 removed outlier: 5.498A pdb=" N MET B4279 " --> pdb=" O THR B4275 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B4298 " --> pdb=" O LEU B4294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B4299 " --> pdb=" O LEU B4295 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL B4301 " --> pdb=" O PHE B4297 " (cutoff:3.500A) Processing helix chain 'B' and resid 4483 through 4499 removed outlier: 5.325A pdb=" N TYR B4487 " --> pdb=" O LYS B4483 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B4492 " --> pdb=" O GLN B4488 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN B4493 " --> pdb=" O GLN B4489 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B4494 " --> pdb=" O LYS B4490 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE B4495 " --> pdb=" O LEU B4491 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA B4496 " --> pdb=" O LEU B4492 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 3.658A pdb=" N LEU B4518 " --> pdb=" O ASN B4514 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4569 through 4612 removed outlier: 3.868A pdb=" N ARG B4573 " --> pdb=" O GLU B4569 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR B4590 " --> pdb=" O CYS B4586 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR B4591 " --> pdb=" O ILE B4587 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU B4593 " --> pdb=" O GLY B4589 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4636 removed outlier: 4.330A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4658 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4675 through 4684 removed outlier: 4.007A pdb=" N GLU B4684 " --> pdb=" O SER B4680 " (cutoff:3.500A) Processing helix chain 'B' and resid 4695 through 4701 removed outlier: 4.441A pdb=" N ILE B4701 " --> pdb=" O VAL B4697 " (cutoff:3.500A) Processing helix chain 'B' and resid 4702 through 4717 removed outlier: 5.562A pdb=" N ASN B4717 " --> pdb=" O VAL B4713 " (cutoff:3.500A) Processing helix chain 'B' and resid 4718 through 4735 removed outlier: 4.111A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.508A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 3.941A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR B4761 " --> pdb=" O LEU B4757 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 4.349A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 4.092A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.203A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4883 Processing helix chain 'B' and resid 4894 through 4902 removed outlier: 4.116A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B4901 " --> pdb=" O TYR B4897 " (cutoff:3.500A) Proline residue: B4902 - end of helix Processing helix chain 'B' and resid 4903 through 4911 removed outlier: 3.824A pdb=" N LEU B4910 " --> pdb=" O GLU B4906 " (cutoff:3.500A) Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 5.593A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TYR B1776 " --> pdb=" O ASN B1773 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B1777 " --> pdb=" O GLU B1774 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1772 through 1778' Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.676A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.670A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 271 removed outlier: 6.616A pdb=" N SER C 268 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 removed outlier: 5.445A pdb=" N THR C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 448 through 464 removed outlier: 3.678A pdb=" N HIS C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 508 removed outlier: 3.589A pdb=" N VAL C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 removed outlier: 3.891A pdb=" N VAL C 517 " --> pdb=" O HIS C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.648A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 555 removed outlier: 4.288A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 563 removed outlier: 4.156A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 5.383A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.590A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.630A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 879 through 901 removed outlier: 4.335A pdb=" N GLU C 883 " --> pdb=" O GLU C 879 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 946 removed outlier: 3.699A pdb=" N SER C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 962 removed outlier: 5.655A pdb=" N LYS C 962 " --> pdb=" O GLU C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 5.126A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 987 removed outlier: 4.203A pdb=" N ILE C 986 " --> pdb=" O ASP C 982 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS C 987 " --> pdb=" O LEU C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 982 through 987' Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1040 through 1061 Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.934A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1226 through 1231 removed outlier: 3.582A pdb=" N GLY C1231 " --> pdb=" O PHE C1227 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 3.958A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.884A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.151A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1640 through 1648' Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.595A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.839A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1723 removed outlier: 4.581A pdb=" N ASN C1723 " --> pdb=" O LEU C1719 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.634A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1803 Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1835 through 1847 Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 4.432A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1951 removed outlier: 4.008A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1954 through 1968 removed outlier: 5.247A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Proline residue: C1968 - end of helix Processing helix chain 'C' and resid 1969 through 1978 Processing helix chain 'C' and resid 1989 through 2008 Processing helix chain 'C' and resid 2057 through 2073 Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.884A pdb=" N GLY C2094 " --> pdb=" O ARG C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.909A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.525A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 3.742A pdb=" N GLY C2181 " --> pdb=" O ASN C2177 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.599A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2218 removed outlier: 3.713A pdb=" N ASP C2216 " --> pdb=" O LYS C2212 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) Processing helix chain 'C' and resid 2219 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 4.060A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C2298 " --> pdb=" O GLU C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2332 through 2337 removed outlier: 3.942A pdb=" N ARG C2336 " --> pdb=" O GLY C2332 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY C2337 " --> pdb=" O PRO C2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2332 through 2337' Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2377 through 2382 removed outlier: 4.721A pdb=" N ILE C2382 " --> pdb=" O GLU C2378 " (cutoff:3.500A) Processing helix chain 'C' and resid 2383 through 2403 Processing helix chain 'C' and resid 2405 through 2412 Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2438 Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 4.196A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2504 removed outlier: 3.767A pdb=" N ASP C2503 " --> pdb=" O ALA C2499 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 3.717A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 5.550A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 5.290A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 Processing helix chain 'C' and resid 2585 through 2596 Processing helix chain 'C' and resid 2603 through 2618 Processing helix chain 'C' and resid 2634 through 2655 Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2694 through 2699 removed outlier: 4.184A pdb=" N GLU C2698 " --> pdb=" O SER C2694 " (cutoff:3.500A) Processing helix chain 'C' and resid 2717 through 2740 Processing helix chain 'C' and resid 2767 through 2786 Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2834 through 2864 removed outlier: 3.873A pdb=" N GLY C2864 " --> pdb=" O LEU C2860 " (cutoff:3.500A) Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.259A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.807A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2915 through 2920 removed outlier: 6.506A pdb=" N LYS C2919 " --> pdb=" O PRO C2915 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG C2920 " --> pdb=" O SER C2916 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2915 through 2920' Processing helix chain 'C' and resid 2925 through 2947 removed outlier: 4.240A pdb=" N ASP C2934 " --> pdb=" O ILE C2930 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU C2935 " --> pdb=" O ARG C2931 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA C2936 " --> pdb=" O TYR C2932 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS C2937 " --> pdb=" O VAL C2933 " (cutoff:3.500A) Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.891A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2997 through 3015 removed outlier: 6.086A pdb=" N GLU C3002 " --> pdb=" O ASN C2998 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE C3008 " --> pdb=" O VAL C3004 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N CYS C3009 " --> pdb=" O THR C3005 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS C3010 " --> pdb=" O SER C3006 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU C3011 " --> pdb=" O LEU C3007 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C3014 " --> pdb=" O LYS C3010 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL C3015 " --> pdb=" O LEU C3011 " (cutoff:3.500A) Processing helix chain 'C' and resid 3017 through 3023 removed outlier: 4.225A pdb=" N LEU C3021 " --> pdb=" O HIS C3017 " (cutoff:3.500A) Processing helix chain 'C' and resid 3024 through 3040 removed outlier: 4.356A pdb=" N SER C3028 " --> pdb=" O ASN C3024 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU C3040 " --> pdb=" O LEU C3036 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3048 Processing helix chain 'C' and resid 3050 through 3077 removed outlier: 4.262A pdb=" N GLN C3077 " --> pdb=" O GLU C3073 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 4.857A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3117 through 3122 Processing helix chain 'C' and resid 3124 through 3143 Processing helix chain 'C' and resid 3145 through 3150 removed outlier: 3.764A pdb=" N GLU C3149 " --> pdb=" O SER C3145 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3145 through 3150' Processing helix chain 'C' and resid 3151 through 3166 removed outlier: 3.636A pdb=" N GLU C3157 " --> pdb=" O SER C3153 " (cutoff:3.500A) Processing helix chain 'C' and resid 3172 through 3180 removed outlier: 4.915A pdb=" N ASP C3176 " --> pdb=" O GLU C3172 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS C3177 " --> pdb=" O THR C3173 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N HIS C3178 " --> pdb=" O HIS C3174 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3182 through 3188 Processing helix chain 'C' and resid 3190 through 3196 removed outlier: 4.800A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 removed outlier: 5.085A pdb=" N CYS C3205 " --> pdb=" O VAL C3201 " (cutoff:3.500A) Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3224 removed outlier: 5.455A pdb=" N ALA C3222 " --> pdb=" O ILE C3218 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU C3223 " --> pdb=" O VAL C3219 " (cutoff:3.500A) Processing helix chain 'C' and resid 3232 through 3254 removed outlier: 4.652A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix removed outlier: 5.165A pdb=" N GLY C3253 " --> pdb=" O TRP C3249 " (cutoff:3.500A) Proline residue: C3254 - end of helix Processing helix chain 'C' and resid 3260 through 3265 removed outlier: 6.589A pdb=" N CYS C3264 " --> pdb=" O ARG C3260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N CYS C3265 " --> pdb=" O ALA C3261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3260 through 3265' Processing helix chain 'C' and resid 3270 through 3291 removed outlier: 5.106A pdb=" N ASN C3274 " --> pdb=" O SER C3270 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C3278 " --> pdb=" O ASN C3274 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP C3291 " --> pdb=" O ASN C3287 " (cutoff:3.500A) Processing helix chain 'C' and resid 3297 through 3307 Proline residue: C3305 - end of helix Processing helix chain 'C' and resid 3311 through 3337 removed outlier: 5.185A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS C3318 " --> pdb=" O LEU C3314 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix Processing helix chain 'C' and resid 3600 through 3606 removed outlier: 6.025A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.961A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3628 Processing helix chain 'C' and resid 3636 through 3647 Proline residue: C3647 - end of helix Processing helix chain 'C' and resid 3649 through 3654 Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.788A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.905A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.200A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 removed outlier: 6.042A pdb=" N ARG C3810 " --> pdb=" O ASN C3806 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C3811 " --> pdb=" O ALA C3807 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3848 Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.870A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.571A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3938 Processing helix chain 'C' and resid 3939 through 3962 removed outlier: 3.662A pdb=" N ALA C3943 " --> pdb=" O ARG C3939 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4027 removed outlier: 4.038A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4029 through 4037 removed outlier: 3.777A pdb=" N TYR C4035 " --> pdb=" O THR C4031 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C4036 " --> pdb=" O PHE C4032 " (cutoff:3.500A) Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.071A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 3.850A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.934A pdb=" N ASP C4093 " --> pdb=" O GLU C4089 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY C4095 " --> pdb=" O ALA C4091 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL C4098 " --> pdb=" O ILE C4094 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 removed outlier: 3.551A pdb=" N PHE C4118 " --> pdb=" O ARG C4114 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4131 Proline residue: C4131 - end of helix Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4183 through 4207 removed outlier: 4.145A pdb=" N GLU C4187 " --> pdb=" O LYS C4183 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4268 removed outlier: 6.896A pdb=" N LYS C4262 " --> pdb=" O MET C4258 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER C4263 " --> pdb=" O LEU C4259 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU C4264 " --> pdb=" O SER C4260 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N MET C4268 " --> pdb=" O LEU C4264 " (cutoff:3.500A) Processing helix chain 'C' and resid 4269 through 4274 Processing helix chain 'C' and resid 4275 through 4310 removed outlier: 5.498A pdb=" N MET C4279 " --> pdb=" O THR C4275 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL C4298 " --> pdb=" O LEU C4294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C4299 " --> pdb=" O LEU C4295 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL C4301 " --> pdb=" O PHE C4297 " (cutoff:3.500A) Processing helix chain 'C' and resid 4483 through 4499 removed outlier: 5.324A pdb=" N TYR C4487 " --> pdb=" O LYS C4483 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C4492 " --> pdb=" O GLN C4488 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN C4493 " --> pdb=" O GLN C4489 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C4494 " --> pdb=" O LYS C4490 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE C4495 " --> pdb=" O LEU C4491 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA C4496 " --> pdb=" O LEU C4492 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 3.658A pdb=" N LEU C4518 " --> pdb=" O ASN C4514 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4569 through 4612 removed outlier: 3.868A pdb=" N ARG C4573 " --> pdb=" O GLU C4569 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR C4590 " --> pdb=" O CYS C4586 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR C4591 " --> pdb=" O ILE C4587 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU C4593 " --> pdb=" O GLY C4589 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4636 removed outlier: 4.330A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4658 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4675 through 4684 removed outlier: 4.007A pdb=" N GLU C4684 " --> pdb=" O SER C4680 " (cutoff:3.500A) Processing helix chain 'C' and resid 4695 through 4701 removed outlier: 4.441A pdb=" N ILE C4701 " --> pdb=" O VAL C4697 " (cutoff:3.500A) Processing helix chain 'C' and resid 4702 through 4717 removed outlier: 5.562A pdb=" N ASN C4717 " --> pdb=" O VAL C4713 " (cutoff:3.500A) Processing helix chain 'C' and resid 4718 through 4735 removed outlier: 4.110A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.509A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 3.940A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR C4761 " --> pdb=" O LEU C4757 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 4.349A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 4.092A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.203A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4883 Processing helix chain 'C' and resid 4894 through 4902 removed outlier: 4.117A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL C4901 " --> pdb=" O TYR C4897 " (cutoff:3.500A) Proline residue: C4902 - end of helix Processing helix chain 'C' and resid 4903 through 4911 removed outlier: 3.823A pdb=" N LEU C4910 " --> pdb=" O GLU C4906 " (cutoff:3.500A) Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 5.593A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR C1776 " --> pdb=" O ASN C1773 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN C1777 " --> pdb=" O GLU C1774 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1772 through 1778' Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 155 through 160 removed outlier: 4.676A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TRP D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 160' Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.670A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 removed outlier: 6.616A pdb=" N SER D 268 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 removed outlier: 5.445A pdb=" N THR D 327 " --> pdb=" O ASP D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 448 through 464 removed outlier: 3.678A pdb=" N HIS D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 508 removed outlier: 3.590A pdb=" N VAL D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 removed outlier: 3.891A pdb=" N VAL D 517 " --> pdb=" O HIS D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.648A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 555 removed outlier: 4.289A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 563 removed outlier: 4.155A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 5.384A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.590A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.631A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 879 through 901 removed outlier: 4.336A pdb=" N GLU D 883 " --> pdb=" O GLU D 879 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 946 removed outlier: 3.698A pdb=" N SER D 936 " --> pdb=" O ASN D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 962 removed outlier: 5.655A pdb=" N LYS D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 5.126A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 987 removed outlier: 4.203A pdb=" N ILE D 986 " --> pdb=" O ASP D 982 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS D 987 " --> pdb=" O LEU D 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 982 through 987' Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1040 through 1061 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.934A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1226 through 1231 removed outlier: 3.583A pdb=" N GLY D1231 " --> pdb=" O PHE D1227 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 3.958A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.884A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.151A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1640 through 1648' Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.596A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.839A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1723 removed outlier: 4.582A pdb=" N ASN D1723 " --> pdb=" O LEU D1719 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.633A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1803 Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1835 through 1847 Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 4.433A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1951 removed outlier: 4.007A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1954 through 1968 removed outlier: 5.246A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Proline residue: D1968 - end of helix Processing helix chain 'D' and resid 1969 through 1978 Processing helix chain 'D' and resid 1989 through 2008 Processing helix chain 'D' and resid 2057 through 2073 Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.882A pdb=" N GLY D2094 " --> pdb=" O ARG D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.909A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.525A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 3.742A pdb=" N GLY D2181 " --> pdb=" O ASN D2177 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.599A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2218 removed outlier: 3.713A pdb=" N ASP D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) Processing helix chain 'D' and resid 2219 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 4.060A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR D2298 " --> pdb=" O GLU D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2332 through 2337 removed outlier: 3.942A pdb=" N ARG D2336 " --> pdb=" O GLY D2332 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY D2337 " --> pdb=" O PRO D2333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2332 through 2337' Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2377 through 2382 removed outlier: 4.721A pdb=" N ILE D2382 " --> pdb=" O GLU D2378 " (cutoff:3.500A) Processing helix chain 'D' and resid 2383 through 2403 Processing helix chain 'D' and resid 2405 through 2412 Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2438 Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 4.197A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2504 removed outlier: 3.767A pdb=" N ASP D2503 " --> pdb=" O ALA D2499 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 3.717A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 5.551A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 5.290A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 Processing helix chain 'D' and resid 2585 through 2596 Processing helix chain 'D' and resid 2603 through 2618 Processing helix chain 'D' and resid 2634 through 2655 Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2694 through 2699 removed outlier: 4.184A pdb=" N GLU D2698 " --> pdb=" O SER D2694 " (cutoff:3.500A) Processing helix chain 'D' and resid 2717 through 2740 Processing helix chain 'D' and resid 2767 through 2786 Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2834 through 2864 removed outlier: 3.873A pdb=" N GLY D2864 " --> pdb=" O LEU D2860 " (cutoff:3.500A) Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.260A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.808A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2915 through 2920 removed outlier: 6.506A pdb=" N LYS D2919 " --> pdb=" O PRO D2915 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG D2920 " --> pdb=" O SER D2916 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2915 through 2920' Processing helix chain 'D' and resid 2925 through 2947 removed outlier: 4.239A pdb=" N ASP D2934 " --> pdb=" O ILE D2930 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU D2935 " --> pdb=" O ARG D2931 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA D2936 " --> pdb=" O TYR D2932 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N HIS D2937 " --> pdb=" O VAL D2933 " (cutoff:3.500A) Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.891A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2997 through 3015 removed outlier: 6.086A pdb=" N GLU D3002 " --> pdb=" O ASN D2998 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE D3008 " --> pdb=" O VAL D3004 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N CYS D3009 " --> pdb=" O THR D3005 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS D3010 " --> pdb=" O SER D3006 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU D3011 " --> pdb=" O LEU D3007 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D3014 " --> pdb=" O LYS D3010 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL D3015 " --> pdb=" O LEU D3011 " (cutoff:3.500A) Processing helix chain 'D' and resid 3017 through 3023 removed outlier: 4.226A pdb=" N LEU D3021 " --> pdb=" O HIS D3017 " (cutoff:3.500A) Processing helix chain 'D' and resid 3024 through 3040 removed outlier: 4.356A pdb=" N SER D3028 " --> pdb=" O ASN D3024 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU D3040 " --> pdb=" O LEU D3036 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3048 Processing helix chain 'D' and resid 3050 through 3077 removed outlier: 4.262A pdb=" N GLN D3077 " --> pdb=" O GLU D3073 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 4.859A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3117 through 3122 Processing helix chain 'D' and resid 3124 through 3143 Processing helix chain 'D' and resid 3145 through 3150 removed outlier: 3.764A pdb=" N GLU D3149 " --> pdb=" O SER D3145 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3145 through 3150' Processing helix chain 'D' and resid 3151 through 3166 removed outlier: 3.637A pdb=" N GLU D3157 " --> pdb=" O SER D3153 " (cutoff:3.500A) Processing helix chain 'D' and resid 3172 through 3180 removed outlier: 4.915A pdb=" N ASP D3176 " --> pdb=" O GLU D3172 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS D3177 " --> pdb=" O THR D3173 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N HIS D3178 " --> pdb=" O HIS D3174 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) Processing helix chain 'D' and resid 3182 through 3188 Processing helix chain 'D' and resid 3190 through 3196 removed outlier: 4.800A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 removed outlier: 5.084A pdb=" N CYS D3205 " --> pdb=" O VAL D3201 " (cutoff:3.500A) Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3224 removed outlier: 5.455A pdb=" N ALA D3222 " --> pdb=" O ILE D3218 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU D3223 " --> pdb=" O VAL D3219 " (cutoff:3.500A) Processing helix chain 'D' and resid 3232 through 3254 removed outlier: 4.652A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix removed outlier: 5.165A pdb=" N GLY D3253 " --> pdb=" O TRP D3249 " (cutoff:3.500A) Proline residue: D3254 - end of helix Processing helix chain 'D' and resid 3260 through 3265 removed outlier: 6.590A pdb=" N CYS D3264 " --> pdb=" O ARG D3260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N CYS D3265 " --> pdb=" O ALA D3261 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3260 through 3265' Processing helix chain 'D' and resid 3270 through 3291 removed outlier: 5.106A pdb=" N ASN D3274 " --> pdb=" O SER D3270 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY D3278 " --> pdb=" O ASN D3274 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP D3291 " --> pdb=" O ASN D3287 " (cutoff:3.500A) Processing helix chain 'D' and resid 3297 through 3307 Proline residue: D3305 - end of helix Processing helix chain 'D' and resid 3311 through 3337 removed outlier: 5.185A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS D3318 " --> pdb=" O LEU D3314 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix Processing helix chain 'D' and resid 3600 through 3606 removed outlier: 6.025A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.960A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3628 Processing helix chain 'D' and resid 3636 through 3647 Proline residue: D3647 - end of helix Processing helix chain 'D' and resid 3649 through 3654 Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.788A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.904A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.199A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 removed outlier: 6.042A pdb=" N ARG D3810 " --> pdb=" O ASN D3806 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN D3811 " --> pdb=" O ALA D3807 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3848 Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.870A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.570A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3938 Processing helix chain 'D' and resid 3939 through 3962 removed outlier: 3.661A pdb=" N ALA D3943 " --> pdb=" O ARG D3939 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4027 removed outlier: 4.038A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4029 through 4037 removed outlier: 3.777A pdb=" N TYR D4035 " --> pdb=" O THR D4031 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP D4036 " --> pdb=" O PHE D4032 " (cutoff:3.500A) Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.071A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 3.849A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.933A pdb=" N ASP D4093 " --> pdb=" O GLU D4089 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY D4095 " --> pdb=" O ALA D4091 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D4098 " --> pdb=" O ILE D4094 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 removed outlier: 3.550A pdb=" N PHE D4118 " --> pdb=" O ARG D4114 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4131 Proline residue: D4131 - end of helix Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4183 through 4207 removed outlier: 4.145A pdb=" N GLU D4187 " --> pdb=" O LYS D4183 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4268 removed outlier: 6.896A pdb=" N LYS D4262 " --> pdb=" O MET D4258 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N SER D4263 " --> pdb=" O LEU D4259 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU D4264 " --> pdb=" O SER D4260 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N MET D4268 " --> pdb=" O LEU D4264 " (cutoff:3.500A) Processing helix chain 'D' and resid 4269 through 4274 Processing helix chain 'D' and resid 4275 through 4310 removed outlier: 5.499A pdb=" N MET D4279 " --> pdb=" O THR D4275 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D4298 " --> pdb=" O LEU D4294 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D4299 " --> pdb=" O LEU D4295 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL D4301 " --> pdb=" O PHE D4297 " (cutoff:3.500A) Processing helix chain 'D' and resid 4483 through 4499 removed outlier: 5.324A pdb=" N TYR D4487 " --> pdb=" O LYS D4483 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D4492 " --> pdb=" O GLN D4488 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASN D4493 " --> pdb=" O GLN D4489 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR D4494 " --> pdb=" O LYS D4490 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE D4495 " --> pdb=" O LEU D4491 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA D4496 " --> pdb=" O LEU D4492 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 3.659A pdb=" N LEU D4518 " --> pdb=" O ASN D4514 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4569 through 4612 removed outlier: 3.868A pdb=" N ARG D4573 " --> pdb=" O GLU D4569 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR D4590 " --> pdb=" O CYS D4586 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR D4591 " --> pdb=" O ILE D4587 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU D4593 " --> pdb=" O GLY D4589 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4636 removed outlier: 4.331A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4658 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4675 through 4684 removed outlier: 4.007A pdb=" N GLU D4684 " --> pdb=" O SER D4680 " (cutoff:3.500A) Processing helix chain 'D' and resid 4695 through 4701 removed outlier: 4.440A pdb=" N ILE D4701 " --> pdb=" O VAL D4697 " (cutoff:3.500A) Processing helix chain 'D' and resid 4702 through 4717 removed outlier: 5.562A pdb=" N ASN D4717 " --> pdb=" O VAL D4713 " (cutoff:3.500A) Processing helix chain 'D' and resid 4718 through 4735 removed outlier: 4.110A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.509A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 3.940A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR D4761 " --> pdb=" O LEU D4757 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 4.349A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 4.092A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.203A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4883 Processing helix chain 'D' and resid 4894 through 4902 removed outlier: 4.116A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL D4901 " --> pdb=" O TYR D4897 " (cutoff:3.500A) Proline residue: D4902 - end of helix Processing helix chain 'D' and resid 4903 through 4911 removed outlier: 3.825A pdb=" N LEU D4910 " --> pdb=" O GLU D4906 " (cutoff:3.500A) Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 5.592A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR D1776 " --> pdb=" O ASN D1773 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN D1777 " --> pdb=" O GLU D1774 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1772 through 1778' Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.780A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.094A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.780A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.094A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.780A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.094A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.780A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.095A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.191A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.444A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= 4, first strand: chain 'A' and resid 193 through 196 Processing sheet with id= 5, first strand: chain 'A' and resid 232 through 235 removed outlier: 3.690A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU A 274 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 13.873A pdb=" N PHE A 295 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N LEU A 308 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 692 through 697 removed outlier: 6.666A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.507A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY A1616 " --> pdb=" O ILE A1611 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 9, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.387A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 902 through 905 Processing sheet with id= 11, first strand: chain 'A' and resid 948 through 952 Processing sheet with id= 12, first strand: chain 'A' and resid 1016 through 1019 removed outlier: 3.851A pdb=" N GLY A1019 " --> pdb=" O ASN A1029 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 3.911A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.651A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.713A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 2787 through 2791 Processing sheet with id= 17, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.899A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 4521 through 4524 Processing sheet with id= 19, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.191A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.444A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= 22, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= 23, first strand: chain 'B' and resid 232 through 235 removed outlier: 3.690A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU B 274 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 13.874A pdb=" N PHE B 295 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N LEU B 308 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 692 through 697 removed outlier: 6.666A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.508A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY B1616 " --> pdb=" O ILE B1611 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 27, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.386A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 902 through 905 Processing sheet with id= 29, first strand: chain 'B' and resid 948 through 952 Processing sheet with id= 30, first strand: chain 'B' and resid 1016 through 1019 removed outlier: 3.852A pdb=" N GLY B1019 " --> pdb=" O ASN B1029 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 3.912A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.652A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 1307 through 1310 removed outlier: 4.713A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 2787 through 2791 Processing sheet with id= 35, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.899A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 4521 through 4524 Processing sheet with id= 37, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.193A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.445A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= 40, first strand: chain 'C' and resid 193 through 196 Processing sheet with id= 41, first strand: chain 'C' and resid 232 through 235 removed outlier: 3.689A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU C 274 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 13.873A pdb=" N PHE C 295 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N LEU C 308 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 692 through 697 removed outlier: 6.666A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.508A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY C1616 " --> pdb=" O ILE C1611 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 45, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.387A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 902 through 905 Processing sheet with id= 47, first strand: chain 'C' and resid 948 through 952 Processing sheet with id= 48, first strand: chain 'C' and resid 1016 through 1019 removed outlier: 3.852A pdb=" N GLY C1019 " --> pdb=" O ASN C1029 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 3.911A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.651A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 1307 through 1310 removed outlier: 4.712A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 2787 through 2791 Processing sheet with id= 53, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.899A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 4521 through 4524 Processing sheet with id= 55, first strand: chain 'D' and resid 47 through 52 removed outlier: 6.192A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.444A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= 58, first strand: chain 'D' and resid 193 through 196 Processing sheet with id= 59, first strand: chain 'D' and resid 232 through 235 removed outlier: 3.690A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU D 274 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 13.874A pdb=" N PHE D 295 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N LEU D 308 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 692 through 697 removed outlier: 6.666A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.507A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY D1616 " --> pdb=" O ILE D1611 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 63, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.387A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 902 through 905 Processing sheet with id= 65, first strand: chain 'D' and resid 948 through 952 Processing sheet with id= 66, first strand: chain 'D' and resid 1016 through 1019 removed outlier: 3.851A pdb=" N GLY D1019 " --> pdb=" O ASN D1029 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 3.911A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.651A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 1307 through 1310 removed outlier: 4.713A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 2787 through 2791 Processing sheet with id= 71, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.899A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 4521 through 4524 Processing sheet with id= 73, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.567A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'E' and resid 46 through 51 removed outlier: 5.068A pdb=" N GLN E 21 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.568A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'F' and resid 46 through 51 removed outlier: 5.068A pdb=" N GLN F 21 " --> pdb=" O ILE F 51 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.567A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'G' and resid 46 through 51 removed outlier: 5.068A pdb=" N GLN G 21 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.568A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'H' and resid 46 through 51 removed outlier: 5.068A pdb=" N GLN H 21 " --> pdb=" O ILE H 51 " (cutoff:3.500A) 7264 hydrogen bonds defined for protein. 21712 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: 103.33 Time building geometry restraints manager: 48.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 23172 1.31 - 1.45: 37654 1.45 - 1.58: 79322 1.58 - 1.71: 52 1.71 - 1.84: 1512 Bond restraints: 141712 Sorted by residual: bond pdb=" CG PRO C3254 " pdb=" CD PRO C3254 " ideal model delta sigma weight residual 1.503 1.301 0.202 3.40e-02 8.65e+02 3.53e+01 bond pdb=" CG PRO B3254 " pdb=" CD PRO B3254 " ideal model delta sigma weight residual 1.503 1.301 0.202 3.40e-02 8.65e+02 3.53e+01 bond pdb=" CG PRO D3254 " pdb=" CD PRO D3254 " ideal model delta sigma weight residual 1.503 1.301 0.202 3.40e-02 8.65e+02 3.52e+01 bond pdb=" CG PRO A3254 " pdb=" CD PRO A3254 " ideal model delta sigma weight residual 1.503 1.302 0.201 3.40e-02 8.65e+02 3.51e+01 bond pdb=" C6 XAN B5004 " pdb=" N1 XAN B5004 " ideal model delta sigma weight residual 1.397 1.322 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 141707 not shown) Histogram of bond angle deviations from ideal: 91.98 - 101.57: 491 101.57 - 111.15: 56275 111.15 - 120.73: 88134 120.73 - 130.32: 45772 130.32 - 139.90: 804 Bond angle restraints: 191476 Sorted by residual: angle pdb=" CB ARG C2793 " pdb=" CG ARG C2793 " pdb=" CD ARG C2793 " ideal model delta sigma weight residual 111.30 129.63 -18.33 2.30e+00 1.89e-01 6.35e+01 angle pdb=" CB ARG B2793 " pdb=" CG ARG B2793 " pdb=" CD ARG B2793 " ideal model delta sigma weight residual 111.30 129.59 -18.29 2.30e+00 1.89e-01 6.32e+01 angle pdb=" CB ARG A2793 " pdb=" CG ARG A2793 " pdb=" CD ARG A2793 " ideal model delta sigma weight residual 111.30 129.58 -18.28 2.30e+00 1.89e-01 6.32e+01 angle pdb=" CB ARG D2793 " pdb=" CG ARG D2793 " pdb=" CD ARG D2793 " ideal model delta sigma weight residual 111.30 129.57 -18.27 2.30e+00 1.89e-01 6.31e+01 angle pdb=" N PRO A3254 " pdb=" CD PRO A3254 " pdb=" CG PRO A3254 " ideal model delta sigma weight residual 103.20 91.98 11.22 1.50e+00 4.44e-01 5.59e+01 ... (remaining 191471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 76165 17.96 - 35.92: 7173 35.92 - 53.89: 1461 53.89 - 71.85: 447 71.85 - 89.81: 178 Dihedral angle restraints: 85424 sinusoidal: 35040 harmonic: 50384 Sorted by residual: dihedral pdb=" CA TYR B4487 " pdb=" C TYR B4487 " pdb=" N GLN B4488 " pdb=" CA GLN B4488 " ideal model delta harmonic sigma weight residual 180.00 143.95 36.05 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA TYR D4487 " pdb=" C TYR D4487 " pdb=" N GLN D4488 " pdb=" CA GLN D4488 " ideal model delta harmonic sigma weight residual 180.00 143.99 36.01 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA TYR C4487 " pdb=" C TYR C4487 " pdb=" N GLN C4488 " pdb=" CA GLN C4488 " ideal model delta harmonic sigma weight residual 180.00 143.99 36.01 0 5.00e+00 4.00e-02 5.19e+01 ... (remaining 85421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 19715 0.086 - 0.172: 1225 0.172 - 0.258: 40 0.258 - 0.344: 8 0.344 - 0.430: 4 Chirality restraints: 20992 Sorted by residual: chirality pdb=" CB ILE A 865 " pdb=" CA ILE A 865 " pdb=" CG1 ILE A 865 " pdb=" CG2 ILE A 865 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CB ILE D 865 " pdb=" CA ILE D 865 " pdb=" CG1 ILE D 865 " pdb=" CG2 ILE D 865 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE B 865 " pdb=" CA ILE B 865 " pdb=" CG1 ILE B 865 " pdb=" CG2 ILE B 865 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 20989 not shown) Planarity restraints: 24600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A4487 " -0.065 2.00e-02 2.50e+03 4.81e-02 4.63e+01 pdb=" CG TYR A4487 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TYR A4487 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A4487 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A4487 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A4487 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A4487 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A4487 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B4487 " 0.065 2.00e-02 2.50e+03 4.81e-02 4.63e+01 pdb=" CG TYR B4487 " -0.117 2.00e-02 2.50e+03 pdb=" CD1 TYR B4487 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B4487 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B4487 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B4487 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B4487 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B4487 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D4487 " -0.065 2.00e-02 2.50e+03 4.81e-02 4.63e+01 pdb=" CG TYR D4487 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TYR D4487 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D4487 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR D4487 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D4487 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D4487 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR D4487 " -0.008 2.00e-02 2.50e+03 ... (remaining 24597 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 771 2.53 - 3.12: 106702 3.12 - 3.72: 227009 3.72 - 4.31: 309626 4.31 - 4.90: 510089 Nonbonded interactions: 1154197 Sorted by model distance: nonbonded pdb=" O PHE B3166 " pdb=" NH1 ARG B3248 " model vdw 1.938 2.520 nonbonded pdb=" O PHE A3166 " pdb=" NH1 ARG A3248 " model vdw 1.939 2.520 nonbonded pdb=" O PHE C3166 " pdb=" NH1 ARG C3248 " model vdw 1.939 2.520 nonbonded pdb=" O PHE D3166 " pdb=" NH1 ARG D3248 " model vdw 1.940 2.520 nonbonded pdb=" OE1 GLU C3172 " pdb=" OH TYR C3245 " model vdw 1.982 2.440 ... (remaining 1154192 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 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.660 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: 0.130 Extract box with map and model: 30.800 Check model and map are aligned: 1.510 Set scattering table: 0.950 Process input model: 461.560 Find NCS groups from input model: 8.360 Set up NCS constraints: 1.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 515.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 0.202 141712 Z= 0.219 Angle : 0.756 18.327 191476 Z= 0.388 Chirality : 0.042 0.430 20992 Planarity : 0.007 0.235 24600 Dihedral : 15.413 89.809 52932 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 1.19 % Allowed : 1.01 % Favored : 97.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.57 (0.06), residues: 17220 helix: 1.42 (0.06), residues: 9000 sheet: -0.05 (0.12), residues: 1756 loop : -0.95 (0.08), residues: 6464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B4481 HIS 0.014 0.001 HIS A3700 PHE 0.055 0.002 PHE D4174 TYR 0.117 0.001 TYR A4487 ARG 0.028 0.001 ARG D3248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 916 time to evaluate : 12.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8038 (mt) REVERT: A 999 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8953 (tt) REVERT: A 2214 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8522 (tpt) REVERT: A 2541 HIS cc_start: 0.7461 (m90) cc_final: 0.7025 (m90) REVERT: A 2681 MET cc_start: 0.6473 (pmm) cc_final: 0.5739 (pmm) REVERT: A 2828 MET cc_start: 0.7005 (mtt) cc_final: 0.6738 (ttm) REVERT: A 2843 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7744 (mmt) REVERT: A 2980 LEU cc_start: 0.8385 (tp) cc_final: 0.8177 (tp) REVERT: A 3022 PHE cc_start: 0.7817 (m-80) cc_final: 0.7403 (m-10) REVERT: A 3072 MET cc_start: 0.8926 (mmt) cc_final: 0.8097 (mmm) REVERT: A 3104 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8193 (ppp) REVERT: A 3134 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 3241 MET cc_start: 0.8907 (mtt) cc_final: 0.8412 (mtt) REVERT: A 3246 MET cc_start: 0.8729 (ptt) cc_final: 0.8492 (ptt) REVERT: A 3257 ASN cc_start: 0.8705 (t0) cc_final: 0.8134 (t0) REVERT: A 3263 MET cc_start: -0.2021 (mpp) cc_final: -0.2414 (mtt) REVERT: A 3279 ASN cc_start: 0.8589 (t160) cc_final: 0.8128 (t0) REVERT: A 3981 MET cc_start: 0.8079 (ttp) cc_final: 0.7805 (ttp) REVERT: A 4174 PHE cc_start: 0.8281 (t80) cc_final: 0.7900 (t80) REVERT: A 4186 MET cc_start: 0.8245 (mmm) cc_final: 0.7655 (mmm) REVERT: A 4200 MET cc_start: 0.8235 (mtt) cc_final: 0.7966 (mtt) REVERT: A 4279 MET cc_start: 0.5402 (ttt) cc_final: 0.5187 (ptm) REVERT: A 4748 MET cc_start: 0.6914 (mmm) cc_final: 0.6679 (mmt) REVERT: E 19 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7951 (mmmt) REVERT: B 28 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 995 MET cc_start: 0.8603 (ppp) cc_final: 0.8355 (tmm) REVERT: B 1694 MET cc_start: 0.8937 (tpt) cc_final: 0.8404 (tpt) REVERT: B 2732 TRP cc_start: 0.8963 (t60) cc_final: 0.8751 (t60) REVERT: B 2754 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6527 (tm-30) REVERT: B 2840 MET cc_start: 0.8904 (mmt) cc_final: 0.8053 (mmm) REVERT: B 2844 MET cc_start: 0.8351 (mpp) cc_final: 0.8016 (mpp) REVERT: B 3159 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8525 (mp) REVERT: B 3241 MET cc_start: 0.8761 (mtt) cc_final: 0.8150 (mmm) REVERT: B 3242 LEU cc_start: 0.9377 (mt) cc_final: 0.9059 (mt) REVERT: B 3263 MET cc_start: 0.0141 (mpp) cc_final: -0.0391 (mtt) REVERT: B 3689 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8301 (mmm) REVERT: B 4055 HIS cc_start: 0.4576 (m90) cc_final: 0.4242 (m90) REVERT: B 4174 PHE cc_start: 0.8322 (t80) cc_final: 0.7884 (t80) REVERT: B 4279 MET cc_start: 0.4959 (ttt) cc_final: 0.4305 (tmm) REVERT: C 81 MET cc_start: 0.8339 (ppp) cc_final: 0.7935 (ppp) REVERT: C 82 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 2162 MET cc_start: 0.8003 (mmp) cc_final: 0.7802 (mmp) REVERT: C 2735 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: C 2939 TYR cc_start: 0.7759 (t80) cc_final: 0.7417 (t80) REVERT: C 3104 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8428 (ppp) REVERT: C 3159 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8248 (mt) REVERT: C 3166 PHE cc_start: 0.8850 (t80) cc_final: 0.7966 (t80) REVERT: C 3241 MET cc_start: 0.8965 (mtt) cc_final: 0.8319 (mmm) REVERT: C 3242 LEU cc_start: 0.9474 (mt) cc_final: 0.9034 (tp) REVERT: C 3263 MET cc_start: -0.0088 (mpp) cc_final: -0.0396 (mtt) REVERT: C 3819 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.5532 (tmm) REVERT: C 3981 MET cc_start: 0.8236 (ttp) cc_final: 0.7772 (ttp) REVERT: D 28 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7307 (tp) REVERT: D 1168 MET cc_start: 0.7470 (ttm) cc_final: 0.7233 (ttt) REVERT: D 1794 MET cc_start: 0.8896 (mtm) cc_final: 0.8606 (mtp) REVERT: D 2541 HIS cc_start: 0.7603 (m90) cc_final: 0.6978 (m90) REVERT: D 2681 MET cc_start: 0.6918 (pmm) cc_final: 0.6609 (pmm) REVERT: D 2732 TRP cc_start: 0.8848 (t60) cc_final: 0.8533 (t60) REVERT: D 2798 MET cc_start: 0.8050 (mmp) cc_final: 0.7845 (mmt) REVERT: D 2980 LEU cc_start: 0.8536 (tp) cc_final: 0.8285 (tp) REVERT: D 3022 PHE cc_start: 0.7862 (m-80) cc_final: 0.7602 (m-10) REVERT: D 3104 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8524 (ptt) REVERT: D 3241 MET cc_start: 0.8956 (mtt) cc_final: 0.8664 (mtt) REVERT: D 3242 LEU cc_start: 0.9161 (mt) cc_final: 0.8798 (mt) REVERT: D 3263 MET cc_start: -0.1272 (mpp) cc_final: -0.2872 (mtt) REVERT: D 3287 ASN cc_start: 0.8416 (m-40) cc_final: 0.8070 (t0) REVERT: D 3319 PHE cc_start: 0.8226 (m-80) cc_final: 0.7922 (m-80) REVERT: D 4019 MET cc_start: 0.8455 (ttt) cc_final: 0.8252 (ttp) REVERT: D 4200 MET cc_start: 0.8348 (mtt) cc_final: 0.8060 (mtt) REVERT: D 4707 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7802 (tmm) outliers start: 180 outliers final: 13 residues processed: 964 average time/residue: 1.2034 time to fit residues: 2046.2874 Evaluate side-chains 804 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 773 time to evaluate : 12.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 2214 MET Chi-restraints excluded: chain A residue 2584 MET Chi-restraints excluded: chain A residue 2843 MET Chi-restraints excluded: chain A residue 3104 MET Chi-restraints excluded: chain A residue 3134 LEU Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 3159 LEU Chi-restraints excluded: chain B residue 3211 LEU Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4707 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 2735 ASP Chi-restraints excluded: chain C residue 3104 MET Chi-restraints excluded: chain C residue 3140 LEU Chi-restraints excluded: chain C residue 3159 LEU Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3819 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 3104 MET Chi-restraints excluded: chain D residue 3134 LEU Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 4707 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 6.9990 chunk 1309 optimal weight: 5.9990 chunk 726 optimal weight: 20.0000 chunk 447 optimal weight: 7.9990 chunk 883 optimal weight: 2.9990 chunk 699 optimal weight: 9.9990 chunk 1354 optimal weight: 7.9990 chunk 524 optimal weight: 8.9990 chunk 823 optimal weight: 8.9990 chunk 1008 optimal weight: 8.9990 chunk 1569 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A1014 GLN ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2071 GLN A2160 ASN ** A2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3279 ASN A3925 GLN A3949 HIS A4643 ASN ** G 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS B1002 ASN ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1146 HIS B2071 GLN B2160 ASN ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3252 HIS ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3308 ASN ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3925 GLN B3931 ASN ** B3949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4643 ASN C 117 HIS ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 ASN ** C1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3925 GLN C3949 HIS C4643 ASN C4787 ASN ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS D1002 ASN ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2160 ASN ** D2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3308 ASN ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3925 GLN D3931 ASN ** D3949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 141712 Z= 0.451 Angle : 0.723 15.991 191476 Z= 0.371 Chirality : 0.044 0.274 20992 Planarity : 0.006 0.104 24600 Dihedral : 6.814 87.722 19113 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 0.46 % Allowed : 5.09 % Favored : 94.45 % 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: 0.43 (0.06), residues: 17220 helix: 1.32 (0.05), residues: 9068 sheet: -0.10 (0.13), residues: 1684 loop : -1.09 (0.08), residues: 6468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B1156 HIS 0.016 0.002 HIS F 26 PHE 0.043 0.002 PHE A3888 TYR 0.057 0.002 TYR D4487 ARG 0.018 0.001 ARG C3248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 886 time to evaluate : 12.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8114 (mt) REVERT: A 935 MET cc_start: 0.8446 (mtp) cc_final: 0.7998 (mtp) REVERT: A 1113 MET cc_start: 0.8559 (mtp) cc_final: 0.8277 (mtt) REVERT: A 1564 MET cc_start: 0.8696 (mmt) cc_final: 0.8435 (mmm) REVERT: A 1975 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8332 (tmm) REVERT: A 2681 MET cc_start: 0.6939 (pmm) cc_final: 0.6266 (pmm) REVERT: A 2732 TRP cc_start: 0.8784 (t60) cc_final: 0.8371 (t60) REVERT: A 2843 MET cc_start: 0.8583 (mtt) cc_final: 0.8343 (ttm) REVERT: A 2858 MET cc_start: 0.8402 (mpp) cc_final: 0.8195 (mpp) REVERT: A 2939 TYR cc_start: 0.8206 (t80) cc_final: 0.7799 (t80) REVERT: A 2980 LEU cc_start: 0.8733 (tp) cc_final: 0.8527 (tp) REVERT: A 3003 MET cc_start: 0.8501 (ptt) cc_final: 0.8213 (ptp) REVERT: A 3022 PHE cc_start: 0.7539 (m-80) cc_final: 0.7270 (m-10) REVERT: A 3068 LEU cc_start: 0.8624 (mt) cc_final: 0.7832 (mt) REVERT: A 3072 MET cc_start: 0.9306 (mmt) cc_final: 0.8642 (mmm) REVERT: A 3104 MET cc_start: 0.8721 (ptp) cc_final: 0.8208 (ppp) REVERT: A 3159 LEU cc_start: 0.9226 (pt) cc_final: 0.8523 (pt) REVERT: A 3241 MET cc_start: 0.8934 (mtt) cc_final: 0.8321 (mmm) REVERT: A 3257 ASN cc_start: 0.8746 (t0) cc_final: 0.8350 (t0) REVERT: A 3819 MET cc_start: 0.6532 (ppp) cc_final: 0.6236 (ppp) REVERT: A 3999 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8294 (mmt) REVERT: A 4174 PHE cc_start: 0.8319 (t80) cc_final: 0.7859 (t80) REVERT: A 4200 MET cc_start: 0.8269 (mtt) cc_final: 0.8023 (mtm) REVERT: A 4504 MET cc_start: 0.7893 (mmp) cc_final: 0.7684 (mmm) REVERT: A 4661 TYR cc_start: 0.7054 (t80) cc_final: 0.6821 (t80) REVERT: A 4707 MET cc_start: 0.7970 (tmm) cc_final: 0.7705 (tpt) REVERT: A 4748 MET cc_start: 0.6979 (mmm) cc_final: 0.6772 (mmt) REVERT: E 67 MET cc_start: 0.9013 (mtt) cc_final: 0.8790 (mtp) REVERT: F 67 MET cc_start: 0.8965 (mtt) cc_final: 0.8709 (mtt) REVERT: H 74 LYS cc_start: 0.8983 (tttt) cc_final: 0.8760 (tttp) REVERT: B 81 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7601 (tmm) REVERT: B 349 MET cc_start: 0.8464 (mmm) cc_final: 0.8095 (mmp) REVERT: B 895 MET cc_start: 0.8511 (mtt) cc_final: 0.8113 (ptp) REVERT: B 995 MET cc_start: 0.8585 (ppp) cc_final: 0.8269 (tmm) REVERT: B 1694 MET cc_start: 0.8928 (tpt) cc_final: 0.8538 (tpt) REVERT: B 2175 MET cc_start: 0.8553 (ttm) cc_final: 0.8278 (ttm) REVERT: B 2214 MET cc_start: 0.9103 (mmm) cc_final: 0.8785 (mmm) REVERT: B 2681 MET cc_start: 0.7302 (pmm) cc_final: 0.6834 (pmm) REVERT: B 2688 MET cc_start: 0.7571 (pmm) cc_final: 0.6797 (pmm) REVERT: B 2840 MET cc_start: 0.8994 (mmm) cc_final: 0.7783 (mmt) REVERT: B 3072 MET cc_start: 0.8364 (mmm) cc_final: 0.8063 (mmt) REVERT: B 3166 PHE cc_start: 0.8828 (t80) cc_final: 0.8418 (t80) REVERT: B 3241 MET cc_start: 0.8866 (mtt) cc_final: 0.8574 (mtp) REVERT: B 3242 LEU cc_start: 0.9330 (mt) cc_final: 0.9102 (mt) REVERT: B 3263 MET cc_start: 0.0639 (mpp) cc_final: -0.0513 (mtm) REVERT: B 3972 MET cc_start: 0.8643 (mmm) cc_final: 0.8163 (mtp) REVERT: B 4174 PHE cc_start: 0.8281 (t80) cc_final: 0.7856 (t80) REVERT: B 4256 MET cc_start: 0.7049 (ppp) cc_final: 0.4550 (mmt) REVERT: B 4568 MET cc_start: 0.7858 (tpp) cc_final: 0.7655 (ttp) REVERT: B 4633 LEU cc_start: 0.8970 (mt) cc_final: 0.8722 (mp) REVERT: C 82 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8066 (mt) REVERT: C 895 MET cc_start: 0.7265 (mtt) cc_final: 0.6247 (ttm) REVERT: C 935 MET cc_start: 0.8361 (mpp) cc_final: 0.8067 (pmm) REVERT: C 1168 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7103 (ttt) REVERT: C 2175 MET cc_start: 0.8487 (ttm) cc_final: 0.8253 (ttm) REVERT: C 2248 MET cc_start: 0.7683 (ttp) cc_final: 0.7477 (ttm) REVERT: C 2721 ILE cc_start: 0.9030 (mt) cc_final: 0.8781 (tt) REVERT: C 2871 LEU cc_start: 0.8586 (tp) cc_final: 0.8319 (tt) REVERT: C 2939 TYR cc_start: 0.8102 (t80) cc_final: 0.7208 (t80) REVERT: C 2943 PHE cc_start: 0.8316 (m-10) cc_final: 0.7737 (m-10) REVERT: C 3104 MET cc_start: 0.8783 (ptp) cc_final: 0.8439 (ptt) REVERT: C 3131 TYR cc_start: 0.8947 (m-80) cc_final: 0.8539 (m-80) REVERT: C 3166 PHE cc_start: 0.8690 (t80) cc_final: 0.7629 (t80) REVERT: C 3241 MET cc_start: 0.8941 (mtt) cc_final: 0.8602 (mtt) REVERT: C 3242 LEU cc_start: 0.9389 (mt) cc_final: 0.9143 (tp) REVERT: C 3263 MET cc_start: 0.0318 (mpp) cc_final: 0.0091 (mtm) REVERT: C 3273 MET cc_start: 0.7641 (mtt) cc_final: 0.7365 (mtp) REVERT: C 3739 MET cc_start: 0.8644 (ttp) cc_final: 0.8379 (ttp) REVERT: C 3819 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6223 (tmm) REVERT: C 3981 MET cc_start: 0.8372 (ttp) cc_final: 0.8032 (ttp) REVERT: C 4258 MET cc_start: 0.4533 (ppp) cc_final: 0.3438 (ptt) REVERT: C 4568 MET cc_start: 0.7640 (ttp) cc_final: 0.7380 (mtm) REVERT: C 4661 TYR cc_start: 0.7260 (t80) cc_final: 0.7055 (t80) REVERT: D 81 MET cc_start: 0.8309 (ppp) cc_final: 0.7854 (ppp) REVERT: D 895 MET cc_start: 0.8730 (mtt) cc_final: 0.8515 (mtt) REVERT: D 995 MET cc_start: 0.8373 (tmm) cc_final: 0.8136 (tmm) REVERT: D 1794 MET cc_start: 0.8934 (mtm) cc_final: 0.8629 (mtp) REVERT: D 2688 MET cc_start: 0.7694 (pmm) cc_final: 0.6888 (pmm) REVERT: D 2689 MET cc_start: 0.7751 (pmm) cc_final: 0.7116 (pmm) REVERT: D 2732 TRP cc_start: 0.8876 (t60) cc_final: 0.8471 (t60) REVERT: D 2760 TYR cc_start: 0.6746 (p90) cc_final: 0.6409 (p90) REVERT: D 2798 MET cc_start: 0.8043 (mmp) cc_final: 0.7680 (mmt) REVERT: D 2835 ARG cc_start: 0.8327 (tpm170) cc_final: 0.8096 (mmm160) REVERT: D 2980 LEU cc_start: 0.8759 (tp) cc_final: 0.8506 (tp) REVERT: D 3014 LEU cc_start: 0.8934 (tp) cc_final: 0.8691 (tt) REVERT: D 3104 MET cc_start: 0.8909 (ptp) cc_final: 0.8547 (ptt) REVERT: D 3241 MET cc_start: 0.9017 (mtt) cc_final: 0.8654 (mtt) REVERT: D 3242 LEU cc_start: 0.9061 (mt) cc_final: 0.8845 (mt) REVERT: D 3273 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7615 (ptt) REVERT: D 3287 ASN cc_start: 0.8473 (m-40) cc_final: 0.8254 (t0) REVERT: D 4200 MET cc_start: 0.8347 (mtt) cc_final: 0.8041 (mtt) outliers start: 70 outliers final: 32 residues processed: 897 average time/residue: 1.1954 time to fit residues: 1888.9430 Evaluate side-chains 855 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 815 time to evaluate : 11.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2798 MET Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 3686 PHE Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 4012 MET Chi-restraints excluded: chain B residue 4487 TYR Chi-restraints excluded: chain B residue 4660 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1168 MET Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 3211 LEU Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 3817 LEU Chi-restraints excluded: chain C residue 3819 MET Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain C residue 4660 PHE Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1037 LEU Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2175 MET Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3273 MET Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 4660 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 3.9990 chunk 487 optimal weight: 8.9990 chunk 1306 optimal weight: 20.0000 chunk 1068 optimal weight: 7.9990 chunk 432 optimal weight: 5.9990 chunk 1572 optimal weight: 20.0000 chunk 1698 optimal weight: 20.0000 chunk 1400 optimal weight: 7.9990 chunk 1558 optimal weight: 6.9990 chunk 535 optimal weight: 1.9990 chunk 1261 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS ** A2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS A4049 HIS ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3931 ASN B3949 HIS ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3806 ASN ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4055 HIS ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 992 GLN D1014 GLN ** D2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN D3949 HIS D4049 HIS ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4643 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 141712 Z= 0.346 Angle : 0.624 14.484 191476 Z= 0.320 Chirality : 0.041 0.210 20992 Planarity : 0.005 0.090 24600 Dihedral : 6.311 88.038 19045 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 0.61 % Allowed : 6.73 % Favored : 92.66 % 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: 0.59 (0.06), residues: 17220 helix: 1.52 (0.06), residues: 9032 sheet: 0.00 (0.13), residues: 1616 loop : -1.10 (0.07), residues: 6572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1156 HIS 0.012 0.001 HIS B3700 PHE 0.036 0.002 PHE A3888 TYR 0.033 0.002 TYR B4487 ARG 0.013 0.001 ARG B4046 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 838 time to evaluate : 12.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8039 (mt) REVERT: A 931 TYR cc_start: 0.9094 (m-10) cc_final: 0.8879 (m-10) REVERT: A 935 MET cc_start: 0.8471 (mtp) cc_final: 0.8032 (mtp) REVERT: A 1960 ARG cc_start: 0.8192 (pmt-80) cc_final: 0.7693 (pmt-80) REVERT: A 2681 MET cc_start: 0.6893 (pmm) cc_final: 0.6666 (pmm) REVERT: A 2732 TRP cc_start: 0.8763 (t60) cc_final: 0.8321 (t60) REVERT: A 2770 ILE cc_start: 0.9194 (mm) cc_final: 0.8942 (mm) REVERT: A 2782 MET cc_start: 0.8486 (mmm) cc_final: 0.8164 (mmm) REVERT: A 2840 MET cc_start: 0.8689 (mmt) cc_final: 0.8377 (mmt) REVERT: A 2843 MET cc_start: 0.8599 (mtt) cc_final: 0.8326 (mtt) REVERT: A 2858 MET cc_start: 0.8420 (mpp) cc_final: 0.8163 (mpp) REVERT: A 2939 TYR cc_start: 0.8139 (t80) cc_final: 0.7810 (t80) REVERT: A 2980 LEU cc_start: 0.8789 (tp) cc_final: 0.8574 (tp) REVERT: A 3003 MET cc_start: 0.8515 (ptt) cc_final: 0.8309 (ptp) REVERT: A 3022 PHE cc_start: 0.7661 (m-80) cc_final: 0.7129 (m-10) REVERT: A 3072 MET cc_start: 0.9354 (mmt) cc_final: 0.8660 (mmm) REVERT: A 3104 MET cc_start: 0.8732 (ptp) cc_final: 0.8222 (ppp) REVERT: A 3131 TYR cc_start: 0.8738 (m-80) cc_final: 0.8185 (m-80) REVERT: A 3159 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8518 (pt) REVERT: A 3166 PHE cc_start: 0.8361 (t80) cc_final: 0.7596 (t80) REVERT: A 3241 MET cc_start: 0.8958 (mtt) cc_final: 0.8240 (mmm) REVERT: A 3257 ASN cc_start: 0.8684 (t0) cc_final: 0.8081 (t0) REVERT: A 3263 MET cc_start: -0.1103 (mtm) cc_final: -0.2416 (mtt) REVERT: A 3819 MET cc_start: 0.6634 (ppp) cc_final: 0.6346 (ppp) REVERT: A 3999 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8338 (mmp) REVERT: A 4057 HIS cc_start: 0.7054 (m90) cc_final: 0.6281 (m170) REVERT: A 4174 PHE cc_start: 0.8242 (t80) cc_final: 0.7792 (t80) REVERT: A 4200 MET cc_start: 0.8282 (mtt) cc_final: 0.8046 (mtm) REVERT: A 4279 MET cc_start: 0.6226 (mpp) cc_final: 0.5946 (mtp) REVERT: A 4748 MET cc_start: 0.6922 (mmm) cc_final: 0.6681 (mmt) REVERT: E 67 MET cc_start: 0.8997 (mtt) cc_final: 0.8792 (mtp) REVERT: H 74 LYS cc_start: 0.8947 (tttt) cc_final: 0.8746 (tttp) REVERT: B 81 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7593 (tmm) REVERT: B 317 MET cc_start: 0.7726 (ptt) cc_final: 0.7351 (ptt) REVERT: B 349 MET cc_start: 0.8484 (mmm) cc_final: 0.8213 (mmp) REVERT: B 935 MET cc_start: 0.8869 (ptt) cc_final: 0.8655 (ptp) REVERT: B 995 MET cc_start: 0.8559 (ppp) cc_final: 0.8267 (tmm) REVERT: B 1694 MET cc_start: 0.8920 (tpt) cc_final: 0.8552 (tpt) REVERT: B 2214 MET cc_start: 0.9083 (mmm) cc_final: 0.8655 (mmm) REVERT: B 2681 MET cc_start: 0.7498 (pmm) cc_final: 0.6946 (pmm) REVERT: B 2840 MET cc_start: 0.9040 (mmt) cc_final: 0.8017 (mmt) REVERT: B 2844 MET cc_start: 0.8232 (mpp) cc_final: 0.8022 (mpp) REVERT: B 3072 MET cc_start: 0.8375 (mmm) cc_final: 0.8091 (mmp) REVERT: B 3166 PHE cc_start: 0.8865 (t80) cc_final: 0.8424 (t80) REVERT: B 3241 MET cc_start: 0.8892 (mtt) cc_final: 0.8360 (mtp) REVERT: B 3972 MET cc_start: 0.8681 (mmm) cc_final: 0.8200 (mtp) REVERT: B 4055 HIS cc_start: 0.5071 (m90) cc_final: 0.3641 (m-70) REVERT: B 4057 HIS cc_start: 0.7373 (m90) cc_final: 0.6808 (m-70) REVERT: B 4174 PHE cc_start: 0.8280 (t80) cc_final: 0.7811 (t80) REVERT: B 4256 MET cc_start: 0.6963 (ppp) cc_final: 0.4330 (mmp) REVERT: B 4707 MET cc_start: 0.8501 (ttm) cc_final: 0.8270 (ttm) REVERT: C 81 MET cc_start: 0.8378 (ppp) cc_final: 0.8103 (ppp) REVERT: C 82 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8176 (mt) REVERT: C 935 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8133 (mpp) REVERT: C 1975 MET cc_start: 0.8745 (ptm) cc_final: 0.8517 (ptp) REVERT: C 2004 MET cc_start: 0.8527 (mmp) cc_final: 0.8159 (mmp) REVERT: C 2175 MET cc_start: 0.8523 (ttm) cc_final: 0.8259 (ttm) REVERT: C 2234 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7171 (ttp) REVERT: C 2721 ILE cc_start: 0.9095 (mt) cc_final: 0.8862 (tt) REVERT: C 3104 MET cc_start: 0.8826 (ptp) cc_final: 0.8563 (ptp) REVERT: C 3131 TYR cc_start: 0.8946 (m-80) cc_final: 0.8562 (m-80) REVERT: C 3134 LEU cc_start: 0.9335 (tt) cc_final: 0.8993 (mt) REVERT: C 3166 PHE cc_start: 0.8812 (t80) cc_final: 0.7827 (t80) REVERT: C 3241 MET cc_start: 0.9036 (mtt) cc_final: 0.8612 (mtt) REVERT: C 3242 LEU cc_start: 0.9570 (mt) cc_final: 0.9223 (tp) REVERT: C 3273 MET cc_start: 0.7616 (mtt) cc_final: 0.7287 (mtp) REVERT: C 3304 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8637 (tp-100) REVERT: C 3739 MET cc_start: 0.8596 (ttp) cc_final: 0.8360 (ttp) REVERT: C 3981 MET cc_start: 0.8387 (ttp) cc_final: 0.8008 (ttp) REVERT: C 3999 MET cc_start: 0.8848 (tpp) cc_final: 0.8547 (tpp) REVERT: C 4052 MET cc_start: 0.8150 (mmm) cc_final: 0.7895 (mmp) REVERT: C 4055 HIS cc_start: 0.4705 (m170) cc_final: 0.4492 (m-70) REVERT: C 4258 MET cc_start: 0.4611 (ppp) cc_final: 0.3696 (ptt) REVERT: C 4279 MET cc_start: 0.6298 (mpp) cc_final: 0.6049 (mmm) REVERT: C 4661 TYR cc_start: 0.7200 (t80) cc_final: 0.6995 (t80) REVERT: D 81 MET cc_start: 0.8105 (ppp) cc_final: 0.7582 (tmm) REVERT: D 964 MET cc_start: 0.6003 (pmm) cc_final: 0.5744 (pmm) REVERT: D 995 MET cc_start: 0.8301 (tmm) cc_final: 0.8042 (tmm) REVERT: D 1794 MET cc_start: 0.8920 (mtm) cc_final: 0.8665 (mtp) REVERT: D 2004 MET cc_start: 0.8544 (mmp) cc_final: 0.8317 (mmp) REVERT: D 2695 MET cc_start: 0.8235 (tmm) cc_final: 0.7798 (tmm) REVERT: D 2732 TRP cc_start: 0.8867 (t60) cc_final: 0.8451 (t60) REVERT: D 2782 MET cc_start: 0.8357 (mmm) cc_final: 0.8129 (mmm) REVERT: D 2798 MET cc_start: 0.8064 (mmp) cc_final: 0.7707 (mmt) REVERT: D 2835 ARG cc_start: 0.8312 (tpm170) cc_final: 0.8093 (mmm160) REVERT: D 2840 MET cc_start: 0.8946 (mmm) cc_final: 0.8566 (mmt) REVERT: D 2844 MET cc_start: 0.8094 (mpp) cc_final: 0.7786 (mmt) REVERT: D 2980 LEU cc_start: 0.8784 (tp) cc_final: 0.8521 (tp) REVERT: D 3072 MET cc_start: 0.9066 (mmt) cc_final: 0.8297 (mmt) REVERT: D 3104 MET cc_start: 0.8855 (ptp) cc_final: 0.8431 (ptt) REVERT: D 3241 MET cc_start: 0.9007 (mtt) cc_final: 0.8653 (mtt) REVERT: D 3287 ASN cc_start: 0.8478 (m-40) cc_final: 0.8255 (t0) REVERT: D 4174 PHE cc_start: 0.7968 (t80) cc_final: 0.7568 (t80) REVERT: D 4186 MET cc_start: 0.9146 (mmm) cc_final: 0.8930 (mmm) REVERT: D 4200 MET cc_start: 0.8404 (mtt) cc_final: 0.8076 (mtt) REVERT: D 4258 MET cc_start: 0.2771 (ptm) cc_final: 0.2499 (ptm) REVERT: D 4292 MET cc_start: 0.6072 (mmt) cc_final: 0.5611 (mmp) REVERT: D 4707 MET cc_start: 0.8465 (ttm) cc_final: 0.8173 (ttm) outliers start: 92 outliers final: 53 residues processed: 883 average time/residue: 1.1608 time to fit residues: 1815.2470 Evaluate side-chains 870 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 810 time to evaluate : 12.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2798 MET Chi-restraints excluded: chain A residue 3159 LEU Chi-restraints excluded: chain A residue 3211 LEU Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2652 LEU Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 2710 ASN Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2821 TYR Chi-restraints excluded: chain B residue 2905 ARG Chi-restraints excluded: chain B residue 3000 GLU Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 4487 TYR Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain B residue 4660 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2234 MET Chi-restraints excluded: chain C residue 2905 ARG Chi-restraints excluded: chain C residue 3000 GLU Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 3817 LEU Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain C residue 4660 PHE Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 3000 GLU Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 4660 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 20.0000 chunk 1181 optimal weight: 20.0000 chunk 815 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 750 optimal weight: 40.0000 chunk 1055 optimal weight: 0.9990 chunk 1577 optimal weight: 0.8980 chunk 1670 optimal weight: 9.9990 chunk 824 optimal weight: 9.9990 chunk 1495 optimal weight: 10.0000 chunk 450 optimal weight: 0.0370 overall best weight: 4.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN ** A2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3077 GLN A3949 HIS ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3949 HIS ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1014 GLN ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 141712 Z= 0.305 Angle : 0.610 16.957 191476 Z= 0.311 Chirality : 0.040 0.212 20992 Planarity : 0.004 0.088 24600 Dihedral : 6.087 89.423 19040 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 0.80 % Allowed : 7.61 % Favored : 91.59 % 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: 0.69 (0.07), residues: 17220 helix: 1.61 (0.06), residues: 9052 sheet: -0.01 (0.13), residues: 1660 loop : -1.07 (0.08), residues: 6508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B4288 HIS 0.011 0.001 HIS B3700 PHE 0.040 0.002 PHE B3162 TYR 0.037 0.002 TYR D2760 ARG 0.009 0.000 ARG B4046 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 818 time to evaluate : 12.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8010 (mt) REVERT: A 931 TYR cc_start: 0.9125 (m-10) cc_final: 0.8905 (m-10) REVERT: A 935 MET cc_start: 0.8521 (mtp) cc_final: 0.8044 (mtp) REVERT: A 1975 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8227 (tmm) REVERT: A 2732 TRP cc_start: 0.8764 (t60) cc_final: 0.8271 (t60) REVERT: A 2770 ILE cc_start: 0.9205 (mm) cc_final: 0.8934 (mm) REVERT: A 2843 MET cc_start: 0.8482 (mtt) cc_final: 0.8208 (mtt) REVERT: A 2939 TYR cc_start: 0.8137 (t80) cc_final: 0.7739 (t80) REVERT: A 2943 PHE cc_start: 0.8611 (m-80) cc_final: 0.8074 (t80) REVERT: A 3072 MET cc_start: 0.9371 (mmt) cc_final: 0.8690 (mmm) REVERT: A 3104 MET cc_start: 0.8721 (ptp) cc_final: 0.8230 (ppp) REVERT: A 3159 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8354 (pt) REVERT: A 3166 PHE cc_start: 0.8369 (t80) cc_final: 0.7743 (t80) REVERT: A 3241 MET cc_start: 0.8902 (mtt) cc_final: 0.8342 (mmm) REVERT: A 3257 ASN cc_start: 0.8638 (t0) cc_final: 0.8218 (t0) REVERT: A 3819 MET cc_start: 0.6664 (ppp) cc_final: 0.6361 (ppp) REVERT: A 3854 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: A 3999 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7962 (mmt) REVERT: A 4057 HIS cc_start: 0.7148 (m90) cc_final: 0.6824 (m170) REVERT: A 4174 PHE cc_start: 0.8259 (t80) cc_final: 0.7836 (t80) REVERT: A 4200 MET cc_start: 0.8344 (mtt) cc_final: 0.8106 (mtm) REVERT: A 4504 MET cc_start: 0.7831 (mmm) cc_final: 0.7628 (mmp) REVERT: E 67 MET cc_start: 0.8986 (mtt) cc_final: 0.8744 (mtp) REVERT: F 67 MET cc_start: 0.8956 (mtp) cc_final: 0.8720 (mtp) REVERT: H 74 LYS cc_start: 0.8953 (tttt) cc_final: 0.8751 (tttp) REVERT: B 81 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7657 (tmm) REVERT: B 317 MET cc_start: 0.7695 (ptt) cc_final: 0.7289 (ptt) REVERT: B 349 MET cc_start: 0.8489 (mmm) cc_final: 0.8181 (mmp) REVERT: B 931 TYR cc_start: 0.9014 (m-10) cc_final: 0.8800 (m-80) REVERT: B 935 MET cc_start: 0.8909 (ptt) cc_final: 0.8662 (ptp) REVERT: B 964 MET cc_start: 0.6414 (pmm) cc_final: 0.6071 (pmm) REVERT: B 995 MET cc_start: 0.8560 (ppp) cc_final: 0.8255 (tmm) REVERT: B 1694 MET cc_start: 0.8900 (tpt) cc_final: 0.8521 (tpt) REVERT: B 2214 MET cc_start: 0.9049 (mmm) cc_final: 0.8660 (mmm) REVERT: B 2681 MET cc_start: 0.7627 (pmm) cc_final: 0.7090 (pmm) REVERT: B 2760 TYR cc_start: 0.6949 (p90) cc_final: 0.6445 (p90) REVERT: B 2840 MET cc_start: 0.9055 (mmt) cc_final: 0.7690 (mmt) REVERT: B 3241 MET cc_start: 0.8839 (mtt) cc_final: 0.8418 (mtt) REVERT: B 3246 MET cc_start: 0.8821 (ptt) cc_final: 0.8287 (ptt) REVERT: B 3273 MET cc_start: 0.7784 (ptt) cc_final: 0.7455 (mtt) REVERT: B 3739 MET cc_start: 0.8820 (ttp) cc_final: 0.8572 (ttp) REVERT: B 4055 HIS cc_start: 0.5267 (m90) cc_final: 0.3924 (m-70) REVERT: B 4057 HIS cc_start: 0.7332 (m90) cc_final: 0.6827 (m-70) REVERT: B 4174 PHE cc_start: 0.8241 (t80) cc_final: 0.7781 (t80) REVERT: B 4568 MET cc_start: 0.7622 (ttm) cc_final: 0.7254 (mtp) REVERT: C 82 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8199 (mt) REVERT: C 935 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8124 (pmm) REVERT: C 1975 MET cc_start: 0.8702 (ptm) cc_final: 0.8498 (ptp) REVERT: C 2175 MET cc_start: 0.8481 (ttm) cc_final: 0.8241 (ttm) REVERT: C 2234 MET cc_start: 0.7521 (ttp) cc_final: 0.7234 (ttp) REVERT: C 2785 TRP cc_start: 0.7880 (m-10) cc_final: 0.7430 (m-90) REVERT: C 2828 MET cc_start: 0.6608 (mtt) cc_final: 0.6369 (mmm) REVERT: C 2840 MET cc_start: 0.9179 (mmm) cc_final: 0.8779 (mmm) REVERT: C 3102 LEU cc_start: 0.8974 (tp) cc_final: 0.8741 (tt) REVERT: C 3104 MET cc_start: 0.8804 (ptp) cc_final: 0.8519 (ptp) REVERT: C 3131 TYR cc_start: 0.8976 (m-80) cc_final: 0.8685 (m-80) REVERT: C 3166 PHE cc_start: 0.8762 (t80) cc_final: 0.7724 (t80) REVERT: C 3239 LEU cc_start: 0.9201 (mp) cc_final: 0.8990 (mm) REVERT: C 3241 MET cc_start: 0.9082 (mtt) cc_final: 0.8815 (mtt) REVERT: C 3242 LEU cc_start: 0.9541 (mt) cc_final: 0.9322 (mt) REVERT: C 3273 MET cc_start: 0.7720 (mtt) cc_final: 0.7387 (mtp) REVERT: C 3304 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8788 (tp-100) REVERT: C 3981 MET cc_start: 0.8366 (ttp) cc_final: 0.7959 (ttp) REVERT: C 3999 MET cc_start: 0.8849 (tpp) cc_final: 0.8521 (tpp) REVERT: C 4052 MET cc_start: 0.8158 (mmm) cc_final: 0.7798 (mmp) REVERT: C 4055 HIS cc_start: 0.4732 (m170) cc_final: 0.4406 (m-70) REVERT: C 4256 MET cc_start: 0.5918 (ptp) cc_final: 0.4456 (mmp) REVERT: C 4258 MET cc_start: 0.4508 (ppp) cc_final: 0.3838 (ptm) REVERT: C 4279 MET cc_start: 0.6278 (mpp) cc_final: 0.6024 (mmm) REVERT: C 4661 TYR cc_start: 0.7183 (t80) cc_final: 0.6950 (t80) REVERT: D 81 MET cc_start: 0.8047 (ppp) cc_final: 0.7508 (tmm) REVERT: D 935 MET cc_start: 0.9078 (ptt) cc_final: 0.8221 (ppp) REVERT: D 964 MET cc_start: 0.6055 (pmm) cc_final: 0.5842 (pmm) REVERT: D 995 MET cc_start: 0.8279 (tmm) cc_final: 0.7888 (tmm) REVERT: D 1729 MET cc_start: 0.8340 (tpp) cc_final: 0.8126 (mmt) REVERT: D 1794 MET cc_start: 0.8909 (mtm) cc_final: 0.8662 (mtp) REVERT: D 2004 MET cc_start: 0.8597 (mmp) cc_final: 0.8289 (mmp) REVERT: D 2695 MET cc_start: 0.8199 (tmm) cc_final: 0.7843 (tmm) REVERT: D 2732 TRP cc_start: 0.8908 (t60) cc_final: 0.8465 (t60) REVERT: D 2782 MET cc_start: 0.8386 (mmm) cc_final: 0.7931 (mmm) REVERT: D 2798 MET cc_start: 0.8101 (mmp) cc_final: 0.7890 (mmt) REVERT: D 2828 MET cc_start: 0.7378 (mtm) cc_final: 0.7134 (ttp) REVERT: D 2980 LEU cc_start: 0.8861 (tp) cc_final: 0.8604 (tp) REVERT: D 3072 MET cc_start: 0.9091 (mmt) cc_final: 0.8235 (mmt) REVERT: D 3104 MET cc_start: 0.8841 (ptp) cc_final: 0.8468 (ptt) REVERT: D 3241 MET cc_start: 0.8980 (mtt) cc_final: 0.8686 (mtt) REVERT: D 3287 ASN cc_start: 0.8464 (m-40) cc_final: 0.8261 (t0) REVERT: D 3999 MET cc_start: 0.8967 (tpp) cc_final: 0.8719 (tpp) REVERT: D 4174 PHE cc_start: 0.7962 (t80) cc_final: 0.7542 (t80) REVERT: D 4200 MET cc_start: 0.8404 (mtt) cc_final: 0.8068 (mtt) REVERT: D 4748 MET cc_start: 0.6879 (mmm) cc_final: 0.6562 (mmm) outliers start: 122 outliers final: 59 residues processed: 897 average time/residue: 1.1720 time to fit residues: 1869.3298 Evaluate side-chains 867 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 800 time to evaluate : 12.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2798 MET Chi-restraints excluded: chain A residue 3000 GLU Chi-restraints excluded: chain A residue 3159 LEU Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4635 ILE Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2417 ILE Chi-restraints excluded: chain B residue 2689 MET Chi-restraints excluded: chain B residue 3000 GLU Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 4487 TYR Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain B residue 4660 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 2760 TYR Chi-restraints excluded: chain C residue 2893 LEU Chi-restraints excluded: chain C residue 3000 GLU Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 4660 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2347 MET Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 3000 GLU Chi-restraints excluded: chain D residue 3175 LEU Chi-restraints excluded: chain D residue 3211 LEU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 3817 LEU Chi-restraints excluded: chain D residue 4511 PHE Chi-restraints excluded: chain D residue 4660 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 50.0000 chunk 948 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 1243 optimal weight: 7.9990 chunk 689 optimal weight: 0.9990 chunk 1425 optimal weight: 7.9990 chunk 1154 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 852 optimal weight: 10.0000 chunk 1499 optimal weight: 10.0000 chunk 421 optimal weight: 0.0670 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS B2727 HIS ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3949 HIS ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2091 GLN ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3077 GLN ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3077 GLN ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 141712 Z= 0.189 Angle : 0.578 13.402 191476 Z= 0.292 Chirality : 0.039 0.214 20992 Planarity : 0.004 0.087 24600 Dihedral : 5.926 89.976 19038 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.62 % Favored : 95.30 % Rotamer: Outliers : 0.61 % Allowed : 8.57 % Favored : 90.82 % 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: 0.84 (0.07), residues: 17220 helix: 1.76 (0.06), residues: 9000 sheet: -0.22 (0.12), residues: 1852 loop : -0.94 (0.08), residues: 6368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B2787 HIS 0.010 0.001 HIS B3700 PHE 0.021 0.001 PHE C4016 TYR 0.035 0.001 TYR A3138 ARG 0.016 0.000 ARG D2835 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 808 time to evaluate : 12.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8011 (mt) REVERT: A 931 TYR cc_start: 0.9173 (m-10) cc_final: 0.8967 (m-10) REVERT: A 935 MET cc_start: 0.8487 (mtp) cc_final: 0.8007 (mtp) REVERT: A 2732 TRP cc_start: 0.8777 (t60) cc_final: 0.8255 (t60) REVERT: A 2770 ILE cc_start: 0.9148 (mm) cc_final: 0.8886 (mm) REVERT: A 2843 MET cc_start: 0.8433 (mtt) cc_final: 0.8162 (mtt) REVERT: A 2939 TYR cc_start: 0.8114 (t80) cc_final: 0.7691 (t80) REVERT: A 2943 PHE cc_start: 0.8622 (m-80) cc_final: 0.8030 (t80) REVERT: A 3072 MET cc_start: 0.9368 (mmt) cc_final: 0.8810 (mmm) REVERT: A 3104 MET cc_start: 0.8684 (ptp) cc_final: 0.8375 (ptm) REVERT: A 3140 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9170 (mt) REVERT: A 3241 MET cc_start: 0.8871 (mtt) cc_final: 0.8470 (mtt) REVERT: A 3245 TYR cc_start: 0.8221 (t80) cc_final: 0.7984 (t80) REVERT: A 3257 ASN cc_start: 0.8646 (t0) cc_final: 0.8116 (t0) REVERT: A 3263 MET cc_start: -0.1517 (mtm) cc_final: -0.3039 (mtt) REVERT: A 3819 MET cc_start: 0.6639 (ppp) cc_final: 0.6347 (ppp) REVERT: A 4057 HIS cc_start: 0.7074 (m90) cc_final: 0.6779 (m170) REVERT: A 4174 PHE cc_start: 0.8306 (t80) cc_final: 0.7879 (t80) REVERT: A 4200 MET cc_start: 0.8347 (mtt) cc_final: 0.8110 (mtm) REVERT: A 4268 MET cc_start: 0.6344 (ttt) cc_final: 0.5829 (tmm) REVERT: A 4279 MET cc_start: 0.5846 (mtp) cc_final: 0.5424 (mpp) REVERT: A 4504 MET cc_start: 0.7817 (mmm) cc_final: 0.7604 (mmp) REVERT: F 67 MET cc_start: 0.8904 (mtp) cc_final: 0.8700 (mtm) REVERT: H 74 LYS cc_start: 0.8938 (tttt) cc_final: 0.8725 (tttp) REVERT: B 81 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7652 (tmm) REVERT: B 317 MET cc_start: 0.7660 (ptt) cc_final: 0.7279 (ptt) REVERT: B 349 MET cc_start: 0.8509 (mmm) cc_final: 0.8201 (mmp) REVERT: B 895 MET cc_start: 0.8469 (mtt) cc_final: 0.8008 (ptp) REVERT: B 931 TYR cc_start: 0.9073 (m-10) cc_final: 0.8855 (m-80) REVERT: B 935 MET cc_start: 0.8885 (ptt) cc_final: 0.8633 (ptp) REVERT: B 964 MET cc_start: 0.6164 (pmm) cc_final: 0.5890 (pmm) REVERT: B 995 MET cc_start: 0.8546 (ppp) cc_final: 0.8254 (tmm) REVERT: B 2214 MET cc_start: 0.9024 (mmm) cc_final: 0.8630 (mmm) REVERT: B 2681 MET cc_start: 0.7584 (pmm) cc_final: 0.7144 (pmm) REVERT: B 2760 TYR cc_start: 0.6740 (p90) cc_final: 0.6470 (p90) REVERT: B 2840 MET cc_start: 0.9006 (mmt) cc_final: 0.8662 (mmt) REVERT: B 2939 TYR cc_start: 0.8072 (t80) cc_final: 0.7450 (t80) REVERT: B 3072 MET cc_start: 0.8529 (mmp) cc_final: 0.8208 (mmt) REVERT: B 3241 MET cc_start: 0.8877 (mtt) cc_final: 0.8361 (mtp) REVERT: B 3263 MET cc_start: -0.1046 (mtm) cc_final: -0.1442 (mtt) REVERT: B 3273 MET cc_start: 0.7564 (ptt) cc_final: 0.7264 (mtt) REVERT: B 3739 MET cc_start: 0.8805 (ttp) cc_final: 0.8529 (ttp) REVERT: B 3854 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: B 4055 HIS cc_start: 0.5228 (m90) cc_final: 0.3992 (m-70) REVERT: B 4057 HIS cc_start: 0.7295 (m90) cc_final: 0.6918 (m-70) REVERT: B 4174 PHE cc_start: 0.8234 (t80) cc_final: 0.7752 (t80) REVERT: B 4256 MET cc_start: 0.6889 (ppp) cc_final: 0.4109 (mmt) REVERT: B 4568 MET cc_start: 0.7608 (ttm) cc_final: 0.7233 (mtp) REVERT: B 4707 MET cc_start: 0.8556 (ttm) cc_final: 0.7869 (tpt) REVERT: C 82 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8185 (mt) REVERT: C 935 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8106 (pmm) REVERT: C 964 MET cc_start: 0.5783 (pmm) cc_final: 0.5457 (pmm) REVERT: C 2175 MET cc_start: 0.8451 (ttm) cc_final: 0.8212 (ttm) REVERT: C 2840 MET cc_start: 0.8990 (mmm) cc_final: 0.8481 (mmt) REVERT: C 2943 PHE cc_start: 0.8269 (m-10) cc_final: 0.7907 (m-10) REVERT: C 3102 LEU cc_start: 0.9014 (tp) cc_final: 0.8766 (tt) REVERT: C 3131 TYR cc_start: 0.8968 (m-80) cc_final: 0.8690 (m-80) REVERT: C 3166 PHE cc_start: 0.8789 (t80) cc_final: 0.7690 (t80) REVERT: C 3241 MET cc_start: 0.9070 (mtt) cc_final: 0.8792 (mtt) REVERT: C 3273 MET cc_start: 0.7719 (mtt) cc_final: 0.7486 (mtt) REVERT: C 3304 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8751 (tp-100) REVERT: C 3888 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8324 (t80) REVERT: C 4052 MET cc_start: 0.8151 (mmm) cc_final: 0.7751 (mmp) REVERT: C 4055 HIS cc_start: 0.4697 (m170) cc_final: 0.4365 (m-70) REVERT: C 4256 MET cc_start: 0.5969 (ptp) cc_final: 0.4523 (mmp) REVERT: C 4258 MET cc_start: 0.4495 (ppp) cc_final: 0.4089 (ptm) REVERT: C 4279 MET cc_start: 0.6204 (mpp) cc_final: 0.5958 (mmm) REVERT: C 4661 TYR cc_start: 0.7145 (t80) cc_final: 0.6888 (t80) REVERT: C 4707 MET cc_start: 0.8189 (ttm) cc_final: 0.7823 (mtt) REVERT: D 81 MET cc_start: 0.7980 (ppp) cc_final: 0.7459 (tmm) REVERT: D 935 MET cc_start: 0.9019 (ptt) cc_final: 0.8169 (ppp) REVERT: D 995 MET cc_start: 0.8256 (tmm) cc_final: 0.7840 (tmm) REVERT: D 1729 MET cc_start: 0.8258 (tpp) cc_final: 0.8031 (mmt) REVERT: D 1794 MET cc_start: 0.8896 (mtm) cc_final: 0.8646 (mtp) REVERT: D 2004 MET cc_start: 0.8578 (mmp) cc_final: 0.8293 (mmp) REVERT: D 2234 MET cc_start: 0.7876 (ttp) cc_final: 0.7673 (ttp) REVERT: D 2732 TRP cc_start: 0.8886 (t60) cc_final: 0.8483 (t60) REVERT: D 2798 MET cc_start: 0.8108 (mmp) cc_final: 0.7881 (mmt) REVERT: D 2828 MET cc_start: 0.7363 (mtm) cc_final: 0.7054 (ttp) REVERT: D 3072 MET cc_start: 0.9103 (mmt) cc_final: 0.8230 (mmt) REVERT: D 3104 MET cc_start: 0.8789 (ptp) cc_final: 0.8441 (ptt) REVERT: D 3241 MET cc_start: 0.8963 (mtt) cc_final: 0.8664 (mtt) REVERT: D 3287 ASN cc_start: 0.8422 (m-40) cc_final: 0.8198 (t0) REVERT: D 4052 MET cc_start: 0.8191 (mmp) cc_final: 0.7874 (mtp) REVERT: D 4174 PHE cc_start: 0.8022 (t80) cc_final: 0.7614 (t80) REVERT: D 4200 MET cc_start: 0.8410 (mtt) cc_final: 0.8081 (mtt) REVERT: D 4661 TYR cc_start: 0.7036 (t80) cc_final: 0.6769 (t80) REVERT: D 4707 MET cc_start: 0.8421 (ttm) cc_final: 0.8164 (ttt) REVERT: D 4748 MET cc_start: 0.6818 (mmm) cc_final: 0.6505 (mmm) outliers start: 93 outliers final: 58 residues processed: 866 average time/residue: 1.1759 time to fit residues: 1811.2905 Evaluate side-chains 858 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 793 time to evaluate : 12.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2798 MET Chi-restraints excluded: chain A residue 3140 LEU Chi-restraints excluded: chain A residue 3256 ASN Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2770 ILE Chi-restraints excluded: chain B residue 2798 MET Chi-restraints excluded: chain B residue 3000 GLU Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 2760 TYR Chi-restraints excluded: chain C residue 2798 MET Chi-restraints excluded: chain C residue 3000 GLU Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 3817 LEU Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain C residue 4635 ILE Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 3000 GLU Chi-restraints excluded: chain D residue 3175 LEU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 3817 LEU Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4511 PHE Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 30.0000 chunk 1504 optimal weight: 10.0000 chunk 330 optimal weight: 40.0000 chunk 980 optimal weight: 30.0000 chunk 412 optimal weight: 9.9990 chunk 1671 optimal weight: 9.9990 chunk 1387 optimal weight: 0.0060 chunk 774 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 553 optimal weight: 8.9990 chunk 877 optimal weight: 3.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2386 ASN B2830 ASN ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3949 HIS ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2091 GLN ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2386 ASN ** D2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 141712 Z= 0.341 Angle : 0.610 14.928 191476 Z= 0.310 Chirality : 0.041 0.215 20992 Planarity : 0.004 0.086 24600 Dihedral : 5.896 86.900 19036 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 0.77 % Allowed : 8.85 % Favored : 90.38 % 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: 0.80 (0.07), residues: 17220 helix: 1.75 (0.06), residues: 9024 sheet: -0.26 (0.12), residues: 1828 loop : -1.00 (0.08), residues: 6368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C2785 HIS 0.012 0.001 HIS C2937 PHE 0.024 0.002 PHE C4174 TYR 0.035 0.002 TYR A3138 ARG 0.009 0.000 ARG B2793 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 824 time to evaluate : 12.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8094 (tp) cc_final: 0.7772 (tp) REVERT: A 82 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8067 (mt) REVERT: A 935 MET cc_start: 0.8568 (mtp) cc_final: 0.8084 (mtp) REVERT: A 2732 TRP cc_start: 0.8783 (t60) cc_final: 0.8284 (t60) REVERT: A 2757 MET cc_start: 0.6163 (mmm) cc_final: 0.5940 (mmm) REVERT: A 2770 ILE cc_start: 0.9201 (mm) cc_final: 0.8948 (mm) REVERT: A 2843 MET cc_start: 0.8468 (mtt) cc_final: 0.8158 (mtt) REVERT: A 2939 TYR cc_start: 0.8127 (t80) cc_final: 0.7712 (t80) REVERT: A 2943 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 3072 MET cc_start: 0.9403 (mmt) cc_final: 0.8865 (mmm) REVERT: A 3104 MET cc_start: 0.8696 (ptp) cc_final: 0.8392 (ptm) REVERT: A 3140 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9207 (mt) REVERT: A 3241 MET cc_start: 0.8893 (mtt) cc_final: 0.8577 (mtp) REVERT: A 3257 ASN cc_start: 0.8728 (t0) cc_final: 0.8191 (t0) REVERT: A 3263 MET cc_start: -0.0524 (mtm) cc_final: -0.1813 (mtt) REVERT: A 3854 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: A 4057 HIS cc_start: 0.7207 (m90) cc_final: 0.6993 (m170) REVERT: A 4174 PHE cc_start: 0.8270 (t80) cc_final: 0.7828 (t80) REVERT: A 4200 MET cc_start: 0.8312 (mtt) cc_final: 0.8076 (mtm) REVERT: A 4268 MET cc_start: 0.6400 (ttt) cc_final: 0.5878 (tmm) REVERT: A 4279 MET cc_start: 0.5936 (mtp) cc_final: 0.5362 (mpp) REVERT: A 4295 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7339 (pp) REVERT: A 4504 MET cc_start: 0.7826 (mmm) cc_final: 0.7616 (mmp) REVERT: H 74 LYS cc_start: 0.8949 (tttt) cc_final: 0.8708 (tttt) REVERT: B 81 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7693 (tmm) REVERT: B 317 MET cc_start: 0.7652 (ptt) cc_final: 0.7262 (ptt) REVERT: B 895 MET cc_start: 0.8525 (mtt) cc_final: 0.8056 (ptp) REVERT: B 935 MET cc_start: 0.8935 (ptt) cc_final: 0.8686 (ptp) REVERT: B 964 MET cc_start: 0.6327 (pmm) cc_final: 0.6047 (pmm) REVERT: B 995 MET cc_start: 0.8570 (ppp) cc_final: 0.8248 (tmm) REVERT: B 2214 MET cc_start: 0.9025 (mmm) cc_final: 0.8636 (mmm) REVERT: B 2681 MET cc_start: 0.7606 (pmm) cc_final: 0.7151 (pmm) REVERT: B 2760 TYR cc_start: 0.6914 (p90) cc_final: 0.6638 (p90) REVERT: B 2828 MET cc_start: 0.7446 (mtt) cc_final: 0.7084 (mtt) REVERT: B 2840 MET cc_start: 0.9031 (mmt) cc_final: 0.8663 (mmt) REVERT: B 2939 TYR cc_start: 0.8087 (t80) cc_final: 0.7479 (t80) REVERT: B 3072 MET cc_start: 0.8497 (mmp) cc_final: 0.8149 (mmt) REVERT: B 3241 MET cc_start: 0.8925 (mtt) cc_final: 0.8378 (mtt) REVERT: B 3263 MET cc_start: -0.0446 (mtm) cc_final: -0.1712 (mtt) REVERT: B 3273 MET cc_start: 0.7735 (ptt) cc_final: 0.7348 (mtt) REVERT: B 3739 MET cc_start: 0.8836 (ttp) cc_final: 0.8537 (ttp) REVERT: B 3854 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: B 4055 HIS cc_start: 0.5310 (m90) cc_final: 0.4052 (m-70) REVERT: B 4057 HIS cc_start: 0.7290 (m90) cc_final: 0.6903 (m-70) REVERT: B 4174 PHE cc_start: 0.8249 (t80) cc_final: 0.7833 (t80) REVERT: B 4256 MET cc_start: 0.6908 (ppp) cc_final: 0.4247 (mmt) REVERT: B 4568 MET cc_start: 0.7670 (ttm) cc_final: 0.7290 (mtp) REVERT: C 82 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8253 (mt) REVERT: C 935 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8145 (mpp) REVERT: C 964 MET cc_start: 0.5810 (pmm) cc_final: 0.5488 (pmm) REVERT: C 1064 LEU cc_start: 0.7853 (mm) cc_final: 0.7557 (mt) REVERT: C 2004 MET cc_start: 0.8631 (mmp) cc_final: 0.8346 (mmm) REVERT: C 2175 MET cc_start: 0.8490 (ttm) cc_final: 0.8255 (ttm) REVERT: C 2234 MET cc_start: 0.7685 (ttm) cc_final: 0.7351 (ttp) REVERT: C 2844 MET cc_start: 0.8490 (mmm) cc_final: 0.8248 (mmm) REVERT: C 2943 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: C 3102 LEU cc_start: 0.9051 (tp) cc_final: 0.8776 (tt) REVERT: C 3131 TYR cc_start: 0.9000 (m-80) cc_final: 0.8794 (m-80) REVERT: C 3166 PHE cc_start: 0.8822 (t80) cc_final: 0.7735 (t80) REVERT: C 3239 LEU cc_start: 0.9215 (mp) cc_final: 0.9006 (mm) REVERT: C 3241 MET cc_start: 0.9057 (mtt) cc_final: 0.8720 (mtt) REVERT: C 3304 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8771 (tp-100) REVERT: C 3888 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8388 (t80) REVERT: C 3981 MET cc_start: 0.8482 (tmm) cc_final: 0.7906 (ttp) REVERT: C 4052 MET cc_start: 0.8196 (mmm) cc_final: 0.7765 (mmp) REVERT: C 4055 HIS cc_start: 0.4796 (m170) cc_final: 0.4464 (m-70) REVERT: C 4256 MET cc_start: 0.5999 (ptp) cc_final: 0.4615 (mmp) REVERT: C 4258 MET cc_start: 0.4474 (ppp) cc_final: 0.4228 (ptm) REVERT: C 4661 TYR cc_start: 0.7162 (t80) cc_final: 0.6904 (t80) REVERT: C 4707 MET cc_start: 0.8184 (ttm) cc_final: 0.7780 (mtt) REVERT: D 81 MET cc_start: 0.7968 (ppp) cc_final: 0.7465 (tmm) REVERT: D 935 MET cc_start: 0.9051 (ptt) cc_final: 0.8278 (ppp) REVERT: D 964 MET cc_start: 0.5950 (pmm) cc_final: 0.5601 (pmm) REVERT: D 995 MET cc_start: 0.8262 (tmm) cc_final: 0.7834 (tmm) REVERT: D 1729 MET cc_start: 0.8279 (tpp) cc_final: 0.8057 (mmt) REVERT: D 1794 MET cc_start: 0.8903 (mtm) cc_final: 0.8678 (mtp) REVERT: D 2004 MET cc_start: 0.8630 (mmp) cc_final: 0.8340 (mmp) REVERT: D 2732 TRP cc_start: 0.8937 (t60) cc_final: 0.8486 (t60) REVERT: D 2798 MET cc_start: 0.8157 (mmp) cc_final: 0.7927 (mmt) REVERT: D 2840 MET cc_start: 0.8804 (mmt) cc_final: 0.8577 (mmt) REVERT: D 3104 MET cc_start: 0.8802 (ptp) cc_final: 0.8464 (ptt) REVERT: D 3241 MET cc_start: 0.8999 (mtt) cc_final: 0.8581 (mtt) REVERT: D 3287 ASN cc_start: 0.8412 (m-40) cc_final: 0.8194 (t0) REVERT: D 4052 MET cc_start: 0.8220 (mmp) cc_final: 0.7867 (mtp) REVERT: D 4174 PHE cc_start: 0.8030 (t80) cc_final: 0.7620 (t80) REVERT: D 4200 MET cc_start: 0.8416 (mtt) cc_final: 0.8086 (mtt) REVERT: D 4661 TYR cc_start: 0.7057 (t80) cc_final: 0.6675 (t80) REVERT: D 4707 MET cc_start: 0.8433 (ttm) cc_final: 0.8166 (ttt) outliers start: 117 outliers final: 78 residues processed: 896 average time/residue: 1.2530 time to fit residues: 2024.9492 Evaluate side-chains 891 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 802 time to evaluate : 12.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2798 MET Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3140 LEU Chi-restraints excluded: chain A residue 3171 LEU Chi-restraints excluded: chain A residue 3256 ASN Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4295 LEU Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4635 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1196 ASP Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2770 ILE Chi-restraints excluded: chain B residue 2798 MET Chi-restraints excluded: chain B residue 3000 GLU Chi-restraints excluded: chain B residue 3178 HIS Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4487 TYR Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 2798 MET Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3000 GLU Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 3817 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain C residue 4635 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 1037 LEU Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 3000 GLU Chi-restraints excluded: chain D residue 3175 LEU Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 3817 LEU Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4511 PHE Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 20.0000 chunk 188 optimal weight: 2.9990 chunk 952 optimal weight: 1.9990 chunk 1220 optimal weight: 6.9990 chunk 945 optimal weight: 0.9980 chunk 1407 optimal weight: 50.0000 chunk 933 optimal weight: 8.9990 chunk 1665 optimal weight: 6.9990 chunk 1042 optimal weight: 7.9990 chunk 1015 optimal weight: 8.9990 chunk 768 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3077 GLN ** A3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3949 HIS ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2938 GLN ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4178 ASN C4558 HIS ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 141712 Z= 0.277 Angle : 0.600 18.629 191476 Z= 0.303 Chirality : 0.040 0.233 20992 Planarity : 0.004 0.086 24600 Dihedral : 5.852 87.811 19036 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.06 % Rotamer: Outliers : 0.68 % Allowed : 9.40 % Favored : 89.91 % 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: 0.82 (0.07), residues: 17220 helix: 1.78 (0.06), residues: 9020 sheet: -0.26 (0.12), residues: 1828 loop : -1.00 (0.08), residues: 6372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D2787 HIS 0.009 0.001 HIS B3700 PHE 0.021 0.001 PHE C4016 TYR 0.039 0.001 TYR A3138 ARG 0.008 0.000 ARG B2793 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 829 time to evaluate : 12.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 349 MET cc_start: 0.8412 (mmp) cc_final: 0.8098 (mmm) REVERT: A 931 TYR cc_start: 0.9090 (m-10) cc_final: 0.8767 (m-80) REVERT: A 935 MET cc_start: 0.8577 (mtp) cc_final: 0.8098 (mtp) REVERT: A 2732 TRP cc_start: 0.8770 (t60) cc_final: 0.8317 (t60) REVERT: A 2770 ILE cc_start: 0.9167 (mm) cc_final: 0.8916 (mm) REVERT: A 2843 MET cc_start: 0.8464 (mtt) cc_final: 0.8151 (mtt) REVERT: A 2939 TYR cc_start: 0.8110 (t80) cc_final: 0.7688 (t80) REVERT: A 2943 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8046 (t80) REVERT: A 3072 MET cc_start: 0.9386 (mmt) cc_final: 0.8876 (mmm) REVERT: A 3104 MET cc_start: 0.8649 (ptp) cc_final: 0.8326 (ptm) REVERT: A 3140 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9211 (mt) REVERT: A 3257 ASN cc_start: 0.8699 (t0) cc_final: 0.8324 (t0) REVERT: A 3819 MET cc_start: 0.6693 (ppp) cc_final: 0.6482 (ppp) REVERT: A 3854 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: A 4057 HIS cc_start: 0.7159 (m90) cc_final: 0.6936 (m170) REVERT: A 4174 PHE cc_start: 0.8286 (t80) cc_final: 0.7863 (t80) REVERT: A 4268 MET cc_start: 0.6372 (ttt) cc_final: 0.5933 (tmm) REVERT: A 4279 MET cc_start: 0.5924 (mtp) cc_final: 0.5035 (mpp) REVERT: A 4295 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7364 (pp) REVERT: A 4504 MET cc_start: 0.7799 (mmm) cc_final: 0.7589 (mmp) REVERT: F 19 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8934 (mmmm) REVERT: B 81 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7604 (tmm) REVERT: B 317 MET cc_start: 0.7674 (ptt) cc_final: 0.7331 (ptt) REVERT: B 895 MET cc_start: 0.8551 (mtt) cc_final: 0.8058 (ptp) REVERT: B 935 MET cc_start: 0.8955 (ptt) cc_final: 0.8707 (ptp) REVERT: B 964 MET cc_start: 0.6334 (pmm) cc_final: 0.6069 (pmm) REVERT: B 995 MET cc_start: 0.8555 (ppp) cc_final: 0.8225 (tmm) REVERT: B 2214 MET cc_start: 0.9023 (mmm) cc_final: 0.8667 (mmm) REVERT: B 2681 MET cc_start: 0.7595 (pmm) cc_final: 0.7203 (pmm) REVERT: B 2695 MET cc_start: 0.8339 (tmm) cc_final: 0.7948 (tmm) REVERT: B 2760 TYR cc_start: 0.6949 (p90) cc_final: 0.6679 (p90) REVERT: B 2840 MET cc_start: 0.9051 (mmt) cc_final: 0.8644 (mmt) REVERT: B 2939 TYR cc_start: 0.8073 (t80) cc_final: 0.7468 (t80) REVERT: B 3072 MET cc_start: 0.8503 (mmp) cc_final: 0.8135 (mmt) REVERT: B 3241 MET cc_start: 0.8923 (mtt) cc_final: 0.8250 (mtt) REVERT: B 3249 TRP cc_start: 0.8322 (m100) cc_final: 0.8059 (m100) REVERT: B 3263 MET cc_start: -0.0691 (mtm) cc_final: -0.1903 (mtt) REVERT: B 3273 MET cc_start: 0.7719 (ptt) cc_final: 0.7314 (mtt) REVERT: B 3739 MET cc_start: 0.8827 (ttp) cc_final: 0.8518 (ttp) REVERT: B 3819 MET cc_start: 0.7043 (ppp) cc_final: 0.6808 (ptp) REVERT: B 3854 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8557 (m-80) REVERT: B 4055 HIS cc_start: 0.5290 (m90) cc_final: 0.4033 (m-70) REVERT: B 4057 HIS cc_start: 0.7293 (m90) cc_final: 0.6980 (m-70) REVERT: B 4174 PHE cc_start: 0.8235 (t80) cc_final: 0.7799 (t80) REVERT: B 4256 MET cc_start: 0.6982 (ppp) cc_final: 0.4315 (mmt) REVERT: B 4568 MET cc_start: 0.7634 (ttm) cc_final: 0.7255 (mtp) REVERT: C 81 MET cc_start: 0.8311 (ppp) cc_final: 0.8006 (ppp) REVERT: C 82 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8210 (mt) REVERT: C 935 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8162 (mpp) REVERT: C 964 MET cc_start: 0.6051 (pmm) cc_final: 0.5678 (pmm) REVERT: C 2004 MET cc_start: 0.8619 (mmp) cc_final: 0.8336 (mmm) REVERT: C 2175 MET cc_start: 0.8479 (ttm) cc_final: 0.8224 (ttm) REVERT: C 2234 MET cc_start: 0.7695 (ttm) cc_final: 0.7366 (ttp) REVERT: C 2840 MET cc_start: 0.8896 (mmm) cc_final: 0.8256 (mmm) REVERT: C 2844 MET cc_start: 0.8479 (mmm) cc_final: 0.8268 (mmm) REVERT: C 2939 TYR cc_start: 0.8171 (t80) cc_final: 0.6646 (t80) REVERT: C 2943 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7887 (m-10) REVERT: C 3003 MET cc_start: 0.8467 (ptt) cc_final: 0.8165 (ptp) REVERT: C 3102 LEU cc_start: 0.9062 (tp) cc_final: 0.8780 (tt) REVERT: C 3131 TYR cc_start: 0.9005 (m-80) cc_final: 0.8794 (m-80) REVERT: C 3166 PHE cc_start: 0.8817 (t80) cc_final: 0.7826 (t80) REVERT: C 3239 LEU cc_start: 0.9198 (mp) cc_final: 0.8996 (mm) REVERT: C 3241 MET cc_start: 0.9031 (mtt) cc_final: 0.8689 (mtt) REVERT: C 3304 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8773 (tp-100) REVERT: C 3888 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8409 (t80) REVERT: C 3981 MET cc_start: 0.8514 (tmm) cc_final: 0.7873 (ttp) REVERT: C 4052 MET cc_start: 0.8153 (mmm) cc_final: 0.7723 (mmp) REVERT: C 4055 HIS cc_start: 0.4700 (m170) cc_final: 0.4377 (m-70) REVERT: C 4256 MET cc_start: 0.5999 (ptp) cc_final: 0.4648 (mmp) REVERT: C 4661 TYR cc_start: 0.7177 (t80) cc_final: 0.6930 (t80) REVERT: C 4707 MET cc_start: 0.8158 (ttm) cc_final: 0.7794 (mtt) REVERT: D 81 MET cc_start: 0.7943 (ppp) cc_final: 0.7495 (tmm) REVERT: D 935 MET cc_start: 0.9055 (ptt) cc_final: 0.8301 (ppp) REVERT: D 964 MET cc_start: 0.5947 (pmm) cc_final: 0.5631 (pmm) REVERT: D 995 MET cc_start: 0.8229 (tmm) cc_final: 0.7935 (tmm) REVERT: D 1721 MET cc_start: 0.7648 (mmm) cc_final: 0.7437 (mmp) REVERT: D 1729 MET cc_start: 0.8268 (tpp) cc_final: 0.8049 (mmt) REVERT: D 1794 MET cc_start: 0.8905 (mtm) cc_final: 0.8671 (mtp) REVERT: D 2004 MET cc_start: 0.8612 (mmp) cc_final: 0.8332 (mmp) REVERT: D 2732 TRP cc_start: 0.8954 (t60) cc_final: 0.8527 (t60) REVERT: D 2798 MET cc_start: 0.8178 (mmp) cc_final: 0.7941 (mmt) REVERT: D 2828 MET cc_start: 0.7602 (mtm) cc_final: 0.7236 (ttp) REVERT: D 2835 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7982 (mmm160) REVERT: D 2844 MET cc_start: 0.8069 (mmp) cc_final: 0.7867 (mmt) REVERT: D 3104 MET cc_start: 0.8780 (ptp) cc_final: 0.8433 (ptt) REVERT: D 3159 LEU cc_start: 0.9075 (tp) cc_final: 0.8631 (pp) REVERT: D 3239 LEU cc_start: 0.8750 (mt) cc_final: 0.8136 (tp) REVERT: D 3241 MET cc_start: 0.8998 (mtt) cc_final: 0.8629 (mtt) REVERT: D 3287 ASN cc_start: 0.8392 (m-40) cc_final: 0.8169 (t0) REVERT: D 4052 MET cc_start: 0.8211 (mmp) cc_final: 0.7831 (mtm) REVERT: D 4174 PHE cc_start: 0.8078 (t80) cc_final: 0.7653 (t80) REVERT: D 4200 MET cc_start: 0.8417 (mtt) cc_final: 0.8090 (mtt) REVERT: D 4268 MET cc_start: 0.6141 (ttt) cc_final: 0.5673 (tmm) REVERT: D 4661 TYR cc_start: 0.7040 (t80) cc_final: 0.6655 (t80) REVERT: D 4884 MET cc_start: 0.7546 (mmp) cc_final: 0.7325 (mmp) outliers start: 104 outliers final: 72 residues processed: 894 average time/residue: 1.1775 time to fit residues: 1874.4263 Evaluate side-chains 892 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 809 time to evaluate : 11.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3140 LEU Chi-restraints excluded: chain A residue 3256 ASN Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4027 THR Chi-restraints excluded: chain A residue 4295 LEU Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4635 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1196 ASP Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2770 ILE Chi-restraints excluded: chain B residue 2798 MET Chi-restraints excluded: chain B residue 3000 GLU Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4012 MET Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1196 ASP Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 2798 MET Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3000 GLU Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 3817 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4027 THR Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain C residue 4635 ILE Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 3000 GLU Chi-restraints excluded: chain D residue 3175 LEU Chi-restraints excluded: chain D residue 3252 HIS Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 3817 LEU Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4511 PHE Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 8.9990 chunk 665 optimal weight: 10.0000 chunk 994 optimal weight: 10.0000 chunk 501 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 322 optimal weight: 1.9990 chunk 1058 optimal weight: 6.9990 chunk 1134 optimal weight: 9.9990 chunk 823 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 1309 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3279 ASN ** A3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS ** A4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2160 ASN ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4178 ASN ** C4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN ** D4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 141712 Z= 0.373 Angle : 0.633 16.478 191476 Z= 0.321 Chirality : 0.041 0.218 20992 Planarity : 0.004 0.085 24600 Dihedral : 5.866 89.932 19036 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 0.74 % Allowed : 9.64 % Favored : 89.62 % 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: 0.79 (0.07), residues: 17220 helix: 1.74 (0.06), residues: 9020 sheet: -0.21 (0.13), residues: 1756 loop : -1.03 (0.08), residues: 6444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D2787 HIS 0.012 0.001 HIS F 26 PHE 0.024 0.002 PHE C4174 TYR 0.043 0.002 TYR A3138 ARG 0.015 0.000 ARG B2793 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 828 time to evaluate : 12.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.8365 (mmp) cc_final: 0.8152 (mmm) REVERT: A 931 TYR cc_start: 0.9083 (m-10) cc_final: 0.8752 (m-80) REVERT: A 935 MET cc_start: 0.8597 (mtp) cc_final: 0.8111 (mtp) REVERT: A 2540 HIS cc_start: 0.6910 (m90) cc_final: 0.6639 (m90) REVERT: A 2732 TRP cc_start: 0.8746 (t60) cc_final: 0.8229 (t60) REVERT: A 2770 ILE cc_start: 0.9176 (mm) cc_final: 0.8927 (mm) REVERT: A 2843 MET cc_start: 0.8486 (mtt) cc_final: 0.8154 (mtt) REVERT: A 2939 TYR cc_start: 0.8139 (t80) cc_final: 0.7695 (t80) REVERT: A 2943 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8062 (t80) REVERT: A 3072 MET cc_start: 0.9392 (mmt) cc_final: 0.8874 (mmm) REVERT: A 3104 MET cc_start: 0.8657 (ptp) cc_final: 0.8340 (ptm) REVERT: A 3140 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9174 (mt) REVERT: A 3257 ASN cc_start: 0.8721 (t0) cc_final: 0.8348 (t0) REVERT: A 3819 MET cc_start: 0.6680 (ppp) cc_final: 0.6389 (ppp) REVERT: A 3854 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: A 4057 HIS cc_start: 0.7222 (m90) cc_final: 0.6954 (m-70) REVERT: A 4174 PHE cc_start: 0.8239 (t80) cc_final: 0.7812 (t80) REVERT: A 4268 MET cc_start: 0.6356 (ttt) cc_final: 0.5935 (tmm) REVERT: A 4295 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7376 (pp) REVERT: A 4504 MET cc_start: 0.7817 (mmm) cc_final: 0.7601 (mmp) REVERT: H 74 LYS cc_start: 0.8910 (tttp) cc_final: 0.8660 (tttt) REVERT: B 81 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7332 (tmm) REVERT: B 317 MET cc_start: 0.7648 (ptt) cc_final: 0.7292 (ptt) REVERT: B 935 MET cc_start: 0.8995 (ptt) cc_final: 0.8746 (ptp) REVERT: B 964 MET cc_start: 0.6422 (pmm) cc_final: 0.6166 (pmm) REVERT: B 995 MET cc_start: 0.8561 (ppp) cc_final: 0.8229 (tmm) REVERT: B 1168 MET cc_start: 0.8090 (mmm) cc_final: 0.7630 (mmm) REVERT: B 2214 MET cc_start: 0.9011 (mmm) cc_final: 0.8690 (mmm) REVERT: B 2681 MET cc_start: 0.7600 (pmm) cc_final: 0.7198 (pmm) REVERT: B 2732 TRP cc_start: 0.9129 (t60) cc_final: 0.8598 (t60) REVERT: B 2760 TYR cc_start: 0.6990 (p90) cc_final: 0.6741 (p90) REVERT: B 2782 MET cc_start: 0.9000 (mmm) cc_final: 0.8777 (mmm) REVERT: B 2939 TYR cc_start: 0.8093 (t80) cc_final: 0.7362 (t80) REVERT: B 3072 MET cc_start: 0.8503 (mmp) cc_final: 0.8149 (mmt) REVERT: B 3241 MET cc_start: 0.8997 (mtt) cc_final: 0.8305 (mtt) REVERT: B 3249 TRP cc_start: 0.8367 (m100) cc_final: 0.8078 (m100) REVERT: B 3263 MET cc_start: -0.0442 (mtm) cc_final: -0.1672 (mtt) REVERT: B 3273 MET cc_start: 0.7736 (ptt) cc_final: 0.7271 (mtt) REVERT: B 3739 MET cc_start: 0.8831 (ttp) cc_final: 0.8533 (ttp) REVERT: B 3854 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: B 4055 HIS cc_start: 0.5341 (m90) cc_final: 0.4067 (m-70) REVERT: B 4057 HIS cc_start: 0.7279 (m90) cc_final: 0.6956 (m-70) REVERT: B 4174 PHE cc_start: 0.8240 (t80) cc_final: 0.7813 (t80) REVERT: B 4256 MET cc_start: 0.7135 (ppp) cc_final: 0.4426 (mmp) REVERT: B 4568 MET cc_start: 0.7637 (ttm) cc_final: 0.7252 (mtp) REVERT: B 4707 MET cc_start: 0.8587 (ttm) cc_final: 0.7929 (tpt) REVERT: C 82 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8262 (mt) REVERT: C 935 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8153 (mpp) REVERT: C 964 MET cc_start: 0.6021 (pmm) cc_final: 0.5649 (pmm) REVERT: C 1057 LEU cc_start: 0.8452 (tp) cc_final: 0.8250 (pp) REVERT: C 2004 MET cc_start: 0.8607 (mmp) cc_final: 0.8307 (mmm) REVERT: C 2175 MET cc_start: 0.8534 (ttm) cc_final: 0.8286 (ttm) REVERT: C 2681 MET cc_start: 0.7671 (pmm) cc_final: 0.7224 (pmm) REVERT: C 2840 MET cc_start: 0.9018 (mmm) cc_final: 0.8511 (mmm) REVERT: C 2844 MET cc_start: 0.8445 (mmm) cc_final: 0.8197 (mmm) REVERT: C 3102 LEU cc_start: 0.9099 (tp) cc_final: 0.8821 (tt) REVERT: C 3166 PHE cc_start: 0.8855 (t80) cc_final: 0.7971 (t80) REVERT: C 3241 MET cc_start: 0.9051 (mtt) cc_final: 0.8603 (mtt) REVERT: C 3304 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8785 (tp-100) REVERT: C 3888 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8404 (t80) REVERT: C 3981 MET cc_start: 0.8522 (tmm) cc_final: 0.7875 (ttp) REVERT: C 4052 MET cc_start: 0.8140 (mmm) cc_final: 0.7700 (mtp) REVERT: C 4256 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.4704 (mmp) REVERT: C 4661 TYR cc_start: 0.7193 (t80) cc_final: 0.6968 (t80) REVERT: C 4707 MET cc_start: 0.8135 (ttm) cc_final: 0.7868 (ttm) REVERT: D 81 MET cc_start: 0.7936 (ppp) cc_final: 0.7515 (tmm) REVERT: D 935 MET cc_start: 0.9067 (ptt) cc_final: 0.8313 (ppp) REVERT: D 964 MET cc_start: 0.6085 (pmm) cc_final: 0.5726 (pmm) REVERT: D 995 MET cc_start: 0.8226 (tmm) cc_final: 0.7919 (tmm) REVERT: D 1729 MET cc_start: 0.8291 (tpp) cc_final: 0.8076 (mmt) REVERT: D 1794 MET cc_start: 0.8904 (mtm) cc_final: 0.8675 (mtp) REVERT: D 2004 MET cc_start: 0.8639 (mmp) cc_final: 0.8338 (mmp) REVERT: D 2939 TYR cc_start: 0.7816 (t80) cc_final: 0.7032 (t80) REVERT: D 3072 MET cc_start: 0.9114 (mmt) cc_final: 0.8341 (mmt) REVERT: D 3104 MET cc_start: 0.8802 (ptp) cc_final: 0.8493 (ptt) REVERT: D 3159 LEU cc_start: 0.9081 (tp) cc_final: 0.8623 (pp) REVERT: D 3241 MET cc_start: 0.9024 (mtt) cc_final: 0.8644 (mtt) REVERT: D 3287 ASN cc_start: 0.8415 (m-40) cc_final: 0.8199 (t0) REVERT: D 4052 MET cc_start: 0.8206 (mmp) cc_final: 0.7800 (mtm) REVERT: D 4174 PHE cc_start: 0.8099 (t80) cc_final: 0.7708 (t80) REVERT: D 4200 MET cc_start: 0.8419 (mtt) cc_final: 0.8081 (mtt) REVERT: D 4268 MET cc_start: 0.6287 (ttt) cc_final: 0.5805 (tmm) REVERT: D 4661 TYR cc_start: 0.7068 (t80) cc_final: 0.6736 (t80) REVERT: D 4884 MET cc_start: 0.7632 (mmp) cc_final: 0.7417 (mmp) outliers start: 112 outliers final: 84 residues processed: 895 average time/residue: 1.1734 time to fit residues: 1867.8113 Evaluate side-chains 904 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 810 time to evaluate : 10.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2821 TYR Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3140 LEU Chi-restraints excluded: chain A residue 3171 LEU Chi-restraints excluded: chain A residue 3256 ASN Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4027 THR Chi-restraints excluded: chain A residue 4295 LEU Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4635 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1196 ASP Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2770 ILE Chi-restraints excluded: chain B residue 3000 GLU Chi-restraints excluded: chain B residue 3178 HIS Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4012 MET Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 1196 ASP Chi-restraints excluded: chain C residue 1271 THR Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 2689 MET Chi-restraints excluded: chain C residue 2798 MET Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3000 GLU Chi-restraints excluded: chain C residue 3178 HIS Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 3817 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4027 THR Chi-restraints excluded: chain C residue 4042 VAL Chi-restraints excluded: chain C residue 4256 MET Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain C residue 4635 ILE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 3000 GLU Chi-restraints excluded: chain D residue 3175 LEU Chi-restraints excluded: chain D residue 3252 HIS Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 3817 LEU Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4511 PHE Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 4.9990 chunk 1595 optimal weight: 30.0000 chunk 1455 optimal weight: 1.9990 chunk 1552 optimal weight: 40.0000 chunk 934 optimal weight: 7.9990 chunk 676 optimal weight: 0.9990 chunk 1218 optimal weight: 0.9980 chunk 476 optimal weight: 0.6980 chunk 1402 optimal weight: 20.0000 chunk 1467 optimal weight: 0.5980 chunk 1546 optimal weight: 30.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 ASN ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS B2091 GLN ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3949 HIS ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 ASN C2091 GLN ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4055 HIS C4057 HIS C4178 ASN ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3931 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 141712 Z= 0.159 Angle : 0.588 16.905 191476 Z= 0.294 Chirality : 0.039 0.217 20992 Planarity : 0.004 0.084 24600 Dihedral : 5.730 88.513 19034 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.35 % Rotamer: Outliers : 0.64 % Allowed : 9.91 % Favored : 89.46 % 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: 0.95 (0.07), residues: 17220 helix: 1.88 (0.06), residues: 8960 sheet: -0.22 (0.13), residues: 1812 loop : -0.91 (0.08), residues: 6448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D2787 HIS 0.009 0.001 HIS C 395 PHE 0.023 0.001 PHE B4016 TYR 0.044 0.001 TYR A3138 ARG 0.014 0.000 ARG B2793 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 812 time to evaluate : 12.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.8385 (mmp) cc_final: 0.8159 (mmm) REVERT: A 931 TYR cc_start: 0.9111 (m-10) cc_final: 0.8802 (m-80) REVERT: A 935 MET cc_start: 0.8584 (mtp) cc_final: 0.8095 (mtp) REVERT: A 2234 MET cc_start: 0.7815 (ptm) cc_final: 0.7470 (ttp) REVERT: A 2540 HIS cc_start: 0.6925 (m90) cc_final: 0.6646 (m90) REVERT: A 2732 TRP cc_start: 0.8736 (t60) cc_final: 0.8232 (t60) REVERT: A 2770 ILE cc_start: 0.9147 (mm) cc_final: 0.8891 (mm) REVERT: A 2798 MET cc_start: 0.8352 (mmm) cc_final: 0.8111 (mmm) REVERT: A 2843 MET cc_start: 0.8428 (mtt) cc_final: 0.8103 (mtt) REVERT: A 2939 TYR cc_start: 0.8092 (t80) cc_final: 0.7641 (t80) REVERT: A 2943 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8063 (t80) REVERT: A 3072 MET cc_start: 0.9371 (mmt) cc_final: 0.8873 (mmm) REVERT: A 3104 MET cc_start: 0.8612 (ptp) cc_final: 0.8288 (ptm) REVERT: A 3140 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9130 (mt) REVERT: A 3241 MET cc_start: 0.8805 (mtt) cc_final: 0.8133 (mmm) REVERT: A 3257 ASN cc_start: 0.8637 (t0) cc_final: 0.8233 (t0) REVERT: A 3819 MET cc_start: 0.6661 (ppp) cc_final: 0.6342 (ppp) REVERT: A 3854 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: A 4174 PHE cc_start: 0.8267 (t80) cc_final: 0.7842 (t80) REVERT: A 4295 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7370 (pp) REVERT: A 4504 MET cc_start: 0.7768 (mmm) cc_final: 0.7554 (mmp) REVERT: A 4661 TYR cc_start: 0.7237 (t80) cc_final: 0.7030 (t80) REVERT: F 19 LYS cc_start: 0.9097 (mmmm) cc_final: 0.8845 (mmmm) REVERT: H 74 LYS cc_start: 0.8887 (tttp) cc_final: 0.8638 (tttt) REVERT: B 81 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7437 (tmm) REVERT: B 317 MET cc_start: 0.7641 (ptt) cc_final: 0.7319 (ptt) REVERT: B 935 MET cc_start: 0.8975 (ptt) cc_final: 0.8732 (ptp) REVERT: B 964 MET cc_start: 0.6265 (pmm) cc_final: 0.6011 (pmm) REVERT: B 995 MET cc_start: 0.8539 (ppp) cc_final: 0.8207 (tmm) REVERT: B 2214 MET cc_start: 0.8994 (mmm) cc_final: 0.8540 (mmm) REVERT: B 2681 MET cc_start: 0.7544 (pmm) cc_final: 0.7154 (pmm) REVERT: B 2732 TRP cc_start: 0.9083 (t60) cc_final: 0.8593 (t60) REVERT: B 2760 TYR cc_start: 0.6954 (p90) cc_final: 0.6678 (p90) REVERT: B 2840 MET cc_start: 0.9069 (mmt) cc_final: 0.8484 (mmm) REVERT: B 2939 TYR cc_start: 0.8069 (t80) cc_final: 0.7317 (t80) REVERT: B 3072 MET cc_start: 0.8461 (mmp) cc_final: 0.8099 (mmt) REVERT: B 3241 MET cc_start: 0.8941 (mtt) cc_final: 0.8277 (mtt) REVERT: B 3263 MET cc_start: -0.0902 (mtm) cc_final: -0.1217 (mtt) REVERT: B 3273 MET cc_start: 0.7618 (ptt) cc_final: 0.7176 (mtt) REVERT: B 3739 MET cc_start: 0.8784 (ttp) cc_final: 0.8485 (ttp) REVERT: B 3819 MET cc_start: 0.7117 (ppp) cc_final: 0.6827 (ptp) REVERT: B 3854 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: B 4055 HIS cc_start: 0.5215 (m90) cc_final: 0.3999 (m-70) REVERT: B 4057 HIS cc_start: 0.7195 (m90) cc_final: 0.6929 (m-70) REVERT: B 4174 PHE cc_start: 0.8243 (t80) cc_final: 0.7822 (t80) REVERT: B 4256 MET cc_start: 0.7063 (ppp) cc_final: 0.4420 (mmp) REVERT: B 4568 MET cc_start: 0.7627 (ttm) cc_final: 0.7277 (mtp) REVERT: B 4661 TYR cc_start: 0.6997 (t80) cc_final: 0.6663 (t80) REVERT: C 82 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8268 (mt) REVERT: C 935 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8121 (mpp) REVERT: C 964 MET cc_start: 0.5934 (pmm) cc_final: 0.5574 (pmm) REVERT: C 2175 MET cc_start: 0.8453 (ttm) cc_final: 0.8233 (ttm) REVERT: C 2681 MET cc_start: 0.7454 (pmm) cc_final: 0.7022 (pmm) REVERT: C 2828 MET cc_start: 0.6897 (mtt) cc_final: 0.6393 (ttp) REVERT: C 2840 MET cc_start: 0.8974 (mmm) cc_final: 0.8449 (mmm) REVERT: C 2844 MET cc_start: 0.8427 (mmm) cc_final: 0.8179 (mmm) REVERT: C 2939 TYR cc_start: 0.7971 (t80) cc_final: 0.6578 (t80) REVERT: C 2943 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7893 (m-10) REVERT: C 3003 MET cc_start: 0.8456 (ptt) cc_final: 0.8139 (ptp) REVERT: C 3102 LEU cc_start: 0.9079 (tp) cc_final: 0.8790 (tt) REVERT: C 3239 LEU cc_start: 0.9175 (mp) cc_final: 0.8943 (mm) REVERT: C 3241 MET cc_start: 0.9019 (mtt) cc_final: 0.8662 (mtt) REVERT: C 3304 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8753 (tp-100) REVERT: C 3888 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8403 (t80) REVERT: C 3981 MET cc_start: 0.8508 (tmm) cc_final: 0.7805 (ttp) REVERT: C 4052 MET cc_start: 0.8195 (mmm) cc_final: 0.7880 (mmp) REVERT: C 4256 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.4693 (mmp) REVERT: C 4661 TYR cc_start: 0.7182 (t80) cc_final: 0.6955 (t80) REVERT: C 4707 MET cc_start: 0.8127 (ttm) cc_final: 0.7844 (ttm) REVERT: C 4728 MET cc_start: 0.8266 (mmm) cc_final: 0.7991 (mmt) REVERT: D 81 MET cc_start: 0.7888 (ppp) cc_final: 0.7535 (tmm) REVERT: D 935 MET cc_start: 0.9061 (ptt) cc_final: 0.8311 (ppp) REVERT: D 964 MET cc_start: 0.5880 (pmm) cc_final: 0.5529 (pmm) REVERT: D 995 MET cc_start: 0.8184 (tmm) cc_final: 0.7682 (tmm) REVERT: D 999 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8863 (mt) REVERT: D 1729 MET cc_start: 0.8234 (tpp) cc_final: 0.8010 (mmt) REVERT: D 1794 MET cc_start: 0.8887 (mtm) cc_final: 0.8654 (mtp) REVERT: D 1906 MET cc_start: 0.8211 (mmm) cc_final: 0.7882 (mmm) REVERT: D 2004 MET cc_start: 0.8604 (mmp) cc_final: 0.8310 (mmp) REVERT: D 2939 TYR cc_start: 0.7757 (t80) cc_final: 0.6972 (t80) REVERT: D 3104 MET cc_start: 0.8758 (ptp) cc_final: 0.8459 (ptt) REVERT: D 3159 LEU cc_start: 0.9046 (tp) cc_final: 0.8596 (pp) REVERT: D 3241 MET cc_start: 0.9011 (mtt) cc_final: 0.8624 (mtt) REVERT: D 3287 ASN cc_start: 0.8340 (m-40) cc_final: 0.8121 (t0) REVERT: D 4052 MET cc_start: 0.8229 (mmp) cc_final: 0.7883 (mtm) REVERT: D 4174 PHE cc_start: 0.8081 (t80) cc_final: 0.7698 (t80) REVERT: D 4200 MET cc_start: 0.8417 (mtt) cc_final: 0.8082 (mtt) REVERT: D 4268 MET cc_start: 0.6314 (ttt) cc_final: 0.5884 (tmm) REVERT: D 4661 TYR cc_start: 0.7030 (t80) cc_final: 0.6717 (t80) outliers start: 97 outliers final: 70 residues processed: 876 average time/residue: 1.1777 time to fit residues: 1838.8528 Evaluate side-chains 882 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 800 time to evaluate : 11.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 949 HIS Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3140 LEU Chi-restraints excluded: chain A residue 3256 ASN Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4027 THR Chi-restraints excluded: chain A residue 4295 LEU Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4635 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2770 ILE Chi-restraints excluded: chain B residue 3000 GLU Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 3888 PHE Chi-restraints excluded: chain B residue 4012 MET Chi-restraints excluded: chain B residue 4042 VAL Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 2798 MET Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3000 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 3817 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4027 THR Chi-restraints excluded: chain C residue 4042 VAL Chi-restraints excluded: chain C residue 4256 MET Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain C residue 4635 ILE Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 3000 GLU Chi-restraints excluded: chain D residue 3175 LEU Chi-restraints excluded: chain D residue 3252 HIS Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 3817 LEU Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain D residue 4027 THR Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4511 PHE Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 6.9990 chunk 1641 optimal weight: 3.9990 chunk 1001 optimal weight: 0.0570 chunk 778 optimal weight: 7.9990 chunk 1140 optimal weight: 0.0050 chunk 1721 optimal weight: 9.9990 chunk 1584 optimal weight: 20.0000 chunk 1370 optimal weight: 6.9990 chunk 142 optimal weight: 0.0870 chunk 1058 optimal weight: 7.9990 chunk 840 optimal weight: 10.0000 overall best weight: 2.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS B2091 GLN B2727 HIS ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3949 HIS ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2091 GLN ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4055 HIS C4178 ASN ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 141712 Z= 0.203 Angle : 0.593 16.597 191476 Z= 0.297 Chirality : 0.039 0.218 20992 Planarity : 0.004 0.082 24600 Dihedral : 5.662 84.738 19034 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 0.57 % Allowed : 10.03 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.99 (0.07), residues: 17220 helix: 1.88 (0.06), residues: 8992 sheet: -0.12 (0.12), residues: 1808 loop : -0.89 (0.08), residues: 6420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D2787 HIS 0.009 0.001 HIS B3700 PHE 0.022 0.001 PHE B4016 TYR 0.050 0.001 TYR A3138 ARG 0.016 0.000 ARG B2793 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34440 Ramachandran restraints generated. 17220 Oldfield, 0 Emsley, 17220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 810 time to evaluate : 10.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.8325 (mmp) cc_final: 0.8103 (mmm) REVERT: A 931 TYR cc_start: 0.9116 (m-10) cc_final: 0.8826 (m-80) REVERT: A 935 MET cc_start: 0.8609 (mtp) cc_final: 0.8120 (mtp) REVERT: A 1906 MET cc_start: 0.8099 (mmm) cc_final: 0.7627 (mmm) REVERT: A 2234 MET cc_start: 0.7767 (ptm) cc_final: 0.7452 (ttp) REVERT: A 2540 HIS cc_start: 0.6926 (m90) cc_final: 0.6634 (m90) REVERT: A 2732 TRP cc_start: 0.8725 (t60) cc_final: 0.8198 (t60) REVERT: A 2770 ILE cc_start: 0.9140 (mm) cc_final: 0.8887 (mm) REVERT: A 2798 MET cc_start: 0.8372 (mmm) cc_final: 0.8139 (mmm) REVERT: A 2843 MET cc_start: 0.8447 (mtt) cc_final: 0.8114 (mtt) REVERT: A 2939 TYR cc_start: 0.8106 (t80) cc_final: 0.7657 (t80) REVERT: A 2943 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 3072 MET cc_start: 0.9377 (mmt) cc_final: 0.8891 (mmm) REVERT: A 3104 MET cc_start: 0.8625 (ptp) cc_final: 0.8299 (ptm) REVERT: A 3140 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9133 (mt) REVERT: A 3257 ASN cc_start: 0.8653 (t0) cc_final: 0.8291 (t0) REVERT: A 3819 MET cc_start: 0.6617 (ppp) cc_final: 0.6302 (ppp) REVERT: A 3854 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: A 4174 PHE cc_start: 0.8266 (t80) cc_final: 0.7857 (t80) REVERT: A 4274 MET cc_start: -0.1185 (mtt) cc_final: -0.1592 (mtt) REVERT: A 4279 MET cc_start: 0.6104 (mpp) cc_final: 0.5380 (mmm) REVERT: A 4295 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7345 (pp) REVERT: A 4504 MET cc_start: 0.7765 (mmm) cc_final: 0.7546 (mmp) REVERT: A 4661 TYR cc_start: 0.7242 (t80) cc_final: 0.5051 (t80) REVERT: F 19 LYS cc_start: 0.9107 (mmmm) cc_final: 0.8863 (mmmm) REVERT: H 74 LYS cc_start: 0.8904 (tttp) cc_final: 0.8649 (tttt) REVERT: B 81 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7389 (tmm) REVERT: B 317 MET cc_start: 0.7645 (ptt) cc_final: 0.7292 (ptt) REVERT: B 895 MET cc_start: 0.8516 (mtt) cc_final: 0.8089 (ptp) REVERT: B 935 MET cc_start: 0.8996 (ptt) cc_final: 0.8745 (ptp) REVERT: B 964 MET cc_start: 0.6235 (pmm) cc_final: 0.5992 (pmm) REVERT: B 995 MET cc_start: 0.8553 (ppp) cc_final: 0.8220 (tmm) REVERT: B 2214 MET cc_start: 0.9137 (mmm) cc_final: 0.8725 (mmm) REVERT: B 2681 MET cc_start: 0.7567 (pmm) cc_final: 0.7170 (pmm) REVERT: B 2732 TRP cc_start: 0.9089 (t60) cc_final: 0.8639 (t60) REVERT: B 2760 TYR cc_start: 0.6984 (p90) cc_final: 0.6703 (p90) REVERT: B 2939 TYR cc_start: 0.8065 (t80) cc_final: 0.7296 (t80) REVERT: B 3072 MET cc_start: 0.8471 (mmp) cc_final: 0.8113 (mmt) REVERT: B 3241 MET cc_start: 0.8962 (mtt) cc_final: 0.8294 (mtt) REVERT: B 3263 MET cc_start: -0.0795 (mtm) cc_final: -0.1099 (mtt) REVERT: B 3273 MET cc_start: 0.7572 (ptt) cc_final: 0.7163 (mtt) REVERT: B 3739 MET cc_start: 0.8798 (ttp) cc_final: 0.8514 (ttp) REVERT: B 3819 MET cc_start: 0.7126 (ppp) cc_final: 0.6817 (ptp) REVERT: B 3854 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: B 4174 PHE cc_start: 0.8237 (t80) cc_final: 0.7818 (t80) REVERT: B 4256 MET cc_start: 0.7110 (ppp) cc_final: 0.4476 (mmp) REVERT: B 4568 MET cc_start: 0.7609 (ttm) cc_final: 0.7260 (mtp) REVERT: B 4661 TYR cc_start: 0.7034 (t80) cc_final: 0.6735 (t80) REVERT: C 82 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8282 (mt) REVERT: C 935 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8139 (mpp) REVERT: C 964 MET cc_start: 0.5887 (pmm) cc_final: 0.5526 (pmm) REVERT: C 2004 MET cc_start: 0.8627 (mmp) cc_final: 0.8347 (mmm) REVERT: C 2175 MET cc_start: 0.8469 (ttm) cc_final: 0.8223 (ttm) REVERT: C 2681 MET cc_start: 0.7516 (pmm) cc_final: 0.7076 (pmm) REVERT: C 2782 MET cc_start: 0.8696 (mmm) cc_final: 0.8445 (tpp) REVERT: C 2828 MET cc_start: 0.6948 (mtt) cc_final: 0.6453 (ttp) REVERT: C 2840 MET cc_start: 0.8990 (mmm) cc_final: 0.8562 (mmm) REVERT: C 2844 MET cc_start: 0.8418 (mmm) cc_final: 0.8213 (mmm) REVERT: C 2939 TYR cc_start: 0.8010 (t80) cc_final: 0.6616 (t80) REVERT: C 2943 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7893 (m-10) REVERT: C 3003 MET cc_start: 0.8452 (ptt) cc_final: 0.8139 (ptp) REVERT: C 3102 LEU cc_start: 0.9123 (tp) cc_final: 0.8848 (tt) REVERT: C 3239 LEU cc_start: 0.9193 (mp) cc_final: 0.8964 (mm) REVERT: C 3241 MET cc_start: 0.9034 (mtt) cc_final: 0.8674 (mtt) REVERT: C 3250 TRP cc_start: 0.7592 (t-100) cc_final: 0.7287 (t-100) REVERT: C 3888 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8427 (t80) REVERT: C 4052 MET cc_start: 0.8170 (mmm) cc_final: 0.7869 (mmp) REVERT: C 4256 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.4707 (mmp) REVERT: C 4661 TYR cc_start: 0.7206 (t80) cc_final: 0.6996 (t80) REVERT: C 4707 MET cc_start: 0.8137 (ttm) cc_final: 0.7859 (ttm) REVERT: D 81 MET cc_start: 0.7876 (ppp) cc_final: 0.7544 (tmm) REVERT: D 935 MET cc_start: 0.9073 (ptt) cc_final: 0.8332 (ppp) REVERT: D 964 MET cc_start: 0.5824 (pmm) cc_final: 0.5480 (pmm) REVERT: D 995 MET cc_start: 0.8179 (tmm) cc_final: 0.7678 (tmm) REVERT: D 999 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8863 (mt) REVERT: D 1729 MET cc_start: 0.8239 (tpp) cc_final: 0.8016 (mmt) REVERT: D 1794 MET cc_start: 0.8895 (mtm) cc_final: 0.8674 (mtp) REVERT: D 2004 MET cc_start: 0.8625 (mmp) cc_final: 0.8322 (mmp) REVERT: D 2732 TRP cc_start: 0.8933 (t60) cc_final: 0.8444 (t60) REVERT: D 2939 TYR cc_start: 0.7808 (t80) cc_final: 0.7027 (t80) REVERT: D 3072 MET cc_start: 0.9109 (mmt) cc_final: 0.8348 (mmt) REVERT: D 3104 MET cc_start: 0.8747 (ptp) cc_final: 0.8447 (ptt) REVERT: D 3159 LEU cc_start: 0.9049 (tp) cc_final: 0.8593 (pp) REVERT: D 3239 LEU cc_start: 0.8856 (mt) cc_final: 0.8279 (tp) REVERT: D 3241 MET cc_start: 0.9018 (mtt) cc_final: 0.8632 (mtt) REVERT: D 3287 ASN cc_start: 0.8348 (m-40) cc_final: 0.8116 (t0) REVERT: D 4052 MET cc_start: 0.8234 (mmp) cc_final: 0.7878 (mtm) REVERT: D 4174 PHE cc_start: 0.8081 (t80) cc_final: 0.7706 (t80) REVERT: D 4200 MET cc_start: 0.8420 (mtt) cc_final: 0.8084 (mtt) REVERT: D 4268 MET cc_start: 0.6382 (ttt) cc_final: 0.5999 (tmm) REVERT: D 4661 TYR cc_start: 0.7078 (t80) cc_final: 0.6764 (t80) REVERT: D 4707 MET cc_start: 0.8450 (ttm) cc_final: 0.8168 (ttt) REVERT: D 4884 MET cc_start: 0.7424 (mmp) cc_final: 0.6967 (mmm) outliers start: 87 outliers final: 67 residues processed: 866 average time/residue: 1.1665 time to fit residues: 1800.2565 Evaluate side-chains 880 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 801 time to evaluate : 11.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2406 MET Chi-restraints excluded: chain A residue 2943 PHE Chi-restraints excluded: chain A residue 3140 LEU Chi-restraints excluded: chain A residue 3256 ASN Chi-restraints excluded: chain A residue 3700 HIS Chi-restraints excluded: chain A residue 3829 VAL Chi-restraints excluded: chain A residue 3854 PHE Chi-restraints excluded: chain A residue 4027 THR Chi-restraints excluded: chain A residue 4295 LEU Chi-restraints excluded: chain A residue 4511 PHE Chi-restraints excluded: chain A residue 4635 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 949 HIS Chi-restraints excluded: chain B residue 1196 ASP Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 2584 MET Chi-restraints excluded: chain B residue 2770 ILE Chi-restraints excluded: chain B residue 3326 LEU Chi-restraints excluded: chain B residue 3817 LEU Chi-restraints excluded: chain B residue 3854 PHE Chi-restraints excluded: chain B residue 4012 MET Chi-restraints excluded: chain B residue 4042 VAL Chi-restraints excluded: chain B residue 4511 PHE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 949 HIS Chi-restraints excluded: chain C residue 2142 MET Chi-restraints excluded: chain C residue 2584 MET Chi-restraints excluded: chain C residue 2798 MET Chi-restraints excluded: chain C residue 2943 PHE Chi-restraints excluded: chain C residue 3000 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3700 HIS Chi-restraints excluded: chain C residue 3817 LEU Chi-restraints excluded: chain C residue 3854 PHE Chi-restraints excluded: chain C residue 3888 PHE Chi-restraints excluded: chain C residue 4042 VAL Chi-restraints excluded: chain C residue 4256 MET Chi-restraints excluded: chain C residue 4511 PHE Chi-restraints excluded: chain C residue 4635 ILE Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 999 LEU Chi-restraints excluded: chain D residue 3000 GLU Chi-restraints excluded: chain D residue 3175 LEU Chi-restraints excluded: chain D residue 3252 HIS Chi-restraints excluded: chain D residue 3700 HIS Chi-restraints excluded: chain D residue 3817 LEU Chi-restraints excluded: chain D residue 3888 PHE Chi-restraints excluded: chain D residue 4027 THR Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4511 PHE Chi-restraints excluded: chain D residue 4520 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 9.9990 chunk 1460 optimal weight: 0.7980 chunk 419 optimal weight: 0.8980 chunk 1264 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 chunk 1373 optimal weight: 9.9990 chunk 574 optimal weight: 9.9990 chunk 1409 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3949 HIS ** B2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3949 HIS ** B4629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4178 ASN ** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.047885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.035205 restraints weight = 1514614.948| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.42 r_work: 0.2820 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 141712 Z= 0.212 Angle : 0.594 17.389 191476 Z= 0.297 Chirality : 0.039 0.218 20992 Planarity : 0.004 0.081 24600 Dihedral : 5.609 82.238 19034 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 0.61 % Allowed : 10.08 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.01 (0.07), residues: 17220 helix: 1.92 (0.06), residues: 8960 sheet: -0.13 (0.13), residues: 1768 loop : -0.89 (0.08), residues: 6492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D2787 HIS 0.016 0.001 HIS D4055 PHE 0.022 0.001 PHE B2943 TYR 0.052 0.001 TYR A3138 ARG 0.014 0.000 ARG B2793 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34277.41 seconds wall clock time: 601 minutes 24.72 seconds (36084.72 seconds total)