Starting phenix.real_space_refine on Thu Mar 21 01:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sep_40424/03_2024/8sep_40424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sep_40424/03_2024/8sep_40424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sep_40424/03_2024/8sep_40424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sep_40424/03_2024/8sep_40424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sep_40424/03_2024/8sep_40424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sep_40424/03_2024/8sep_40424_updated.pdb" } resolution = 3.57 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= -0.002 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 8 5.49 5 S 960 5.16 5 C 90996 2.51 5 N 24700 2.21 5 O 26432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4966": "OD1" <-> "OD2" Residue "B TYR 4173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4966": "OD1" <-> "OD2" Residue "C TYR 4173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4966": "OD1" <-> "OD2" Residue "D TYR 4173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4966": "OD1" <-> "OD2" Time to flip residues: 0.42s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143100 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 34929 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4379, 34866 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4162} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4379, 34866 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4162} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35578 Chain: "B" Number of atoms: 34929 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4379, 34866 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4162} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4379, 34866 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4162} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35578 Chain: "C" Number of atoms: 34929 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4379, 34866 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4162} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4379, 34866 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4162} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35578 Chain: "D" Number of atoms: 34929 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4379, 34866 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4162} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 4379, 34866 Classifications: {'peptide': 4379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4162} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35578 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34255 SG CYS A4958 176.935 203.253 87.248 1.00143.26 S ATOM 34280 SG CYS A4961 179.403 203.529 90.045 1.00134.39 S ATOM 69184 SG CYS B4958 180.515 176.953 87.250 1.00143.26 S ATOM 69209 SG CYS B4961 180.241 179.421 90.048 1.00134.39 S ATOM A0369 SG CYS C4958 206.872 180.519 87.251 1.00143.26 S ATOM A036Y SG CYS C4961 204.404 180.244 90.049 1.00134.39 S ATOM A0U4I SG CYS D4958 203.306 206.875 87.249 1.00143.26 S ATOM A0U57 SG CYS D4961 203.581 204.407 90.047 1.00134.39 S Time building chain proxies: 99.94, per 1000 atoms: 0.70 Number of scatterers: 143100 At special positions: 0 Unit cell: (385.112, 385.112, 209.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 960 16.00 P 8 15.00 O 26432 8.00 N 24700 7.00 C 90996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A3170 " - pdb=" SG CYS A3240 " distance=2.03 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B3170 " - pdb=" SG CYS B3240 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C3170 " - pdb=" SG CYS C3240 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D 230 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D3170 " - pdb=" SG CYS D3240 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.39 Conformation dependent library (CDL) restraints added in 36.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33696 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: 684 helices and 72 sheets defined 58.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 43.15 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 4.221A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.520A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 255' Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.928A pdb=" N ALA A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.756A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 423 removed outlier: 3.695A pdb=" N HIS A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 453 Processing helix chain 'A' and resid 461 through 482 removed outlier: 3.763A pdb=" N GLN A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.518A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.085A pdb=" N TYR A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 removed outlier: 4.520A pdb=" N LYS A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 544 removed outlier: 3.863A pdb=" N PHE A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.758A pdb=" N LYS A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 4.239A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 570 " --> pdb=" O CYS A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.999A pdb=" N ASN A 576 " --> pdb=" O PRO A 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 577 " --> pdb=" O GLU A 573 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 579' Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.775A pdb=" N LEU A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 4.052A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 629 removed outlier: 4.242A pdb=" N LEU A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Proline residue: A 627 - end of helix Processing helix chain 'A' and resid 810 through 815 removed outlier: 4.680A pdb=" N ALA A 814 " --> pdb=" O PRO A 810 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 815 " --> pdb=" O CYS A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 815' Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.951A pdb=" N PHE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 852 " --> pdb=" O HIS A 848 " (cutoff:3.500A) Proline residue: A 853 - end of helix No H-bonds generated for 'chain 'A' and resid 847 through 853' Processing helix chain 'A' and resid 864 through 885 removed outlier: 3.532A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 881 " --> pdb=" O ASN A 877 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TRP A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.812A pdb=" N LEU A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Proline residue: A 914 - end of helix No H-bonds generated for 'chain 'A' and resid 909 through 914' Processing helix chain 'A' and resid 915 through 936 Processing helix chain 'A' and resid 945 through 950 removed outlier: 3.919A pdb=" N ASN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1004 removed outlier: 3.524A pdb=" N VAL A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1048 removed outlier: 4.041A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 4.634A pdb=" N ARG A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1067 through 1072' Processing helix chain 'A' and resid 1207 through 1212 removed outlier: 3.942A pdb=" N LEU A1211 " --> pdb=" O ASP A1207 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG A1212 " --> pdb=" O VAL A1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1207 through 1212' Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 3.727A pdb=" N GLY A1218 " --> pdb=" O PHE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1430 removed outlier: 3.583A pdb=" N LEU A1428 " --> pdb=" O PRO A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1449 removed outlier: 3.932A pdb=" N VAL A1448 " --> pdb=" O GLU A1444 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TRP A1449 " --> pdb=" O PRO A1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1444 through 1449' Processing helix chain 'A' and resid 1496 through 1501 removed outlier: 4.588A pdb=" N PHE A1500 " --> pdb=" O TRP A1496 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1496 through 1501' Processing helix chain 'A' and resid 1574 through 1581 removed outlier: 3.802A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A1580 " --> pdb=" O SER A1576 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1657 removed outlier: 4.260A pdb=" N LEU A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A1654 " --> pdb=" O ILE A1650 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU A1655 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A1657 " --> pdb=" O LEU A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 3.758A pdb=" N PHE A1662 " --> pdb=" O ASP A1658 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A1674 " --> pdb=" O TYR A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1689 removed outlier: 3.530A pdb=" N CYS A1686 " --> pdb=" O ALA A1682 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1700 removed outlier: 3.624A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1719 Processing helix chain 'A' and resid 1720 through 1734 removed outlier: 3.993A pdb=" N SER A1732 " --> pdb=" O ARG A1728 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A1733 " --> pdb=" O SER A1729 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N TYR A1734 " --> pdb=" O MET A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.836A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1825 removed outlier: 3.642A pdb=" N HIS A1825 " --> pdb=" O ASP A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1855 through 1867 Processing helix chain 'A' and resid 1925 through 1930 removed outlier: 4.323A pdb=" N MET A1929 " --> pdb=" O GLY A1925 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS A1930 " --> pdb=" O LEU A1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1925 through 1930' Processing helix chain 'A' and resid 1934 through 1987 removed outlier: 3.828A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A1945 " --> pdb=" O ASN A1941 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A1982 " --> pdb=" O ALA A1978 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A1984 " --> pdb=" O LEU A1980 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR A1985 " --> pdb=" O MET A1981 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET A1986 " --> pdb=" O ARG A1982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1990 through 2000 removed outlier: 4.256A pdb=" N ARG A1994 " --> pdb=" O GLU A1990 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU A1997 " --> pdb=" O ARG A1993 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2001 through 2011 removed outlier: 3.697A pdb=" N ASN A2007 " --> pdb=" O GLN A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2017 through 2022 removed outlier: 3.539A pdb=" N CYS A2021 " --> pdb=" O ASP A2017 " (cutoff:3.500A) Proline residue: A2022 - end of helix No H-bonds generated for 'chain 'A' and resid 2017 through 2022' Processing helix chain 'A' and resid 2024 through 2043 Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.612A pdb=" N SER A2099 " --> pdb=" O GLN A2095 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 4.114A pdb=" N GLY A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2142 Proline residue: A2139 - end of helix removed outlier: 5.390A pdb=" N TYR A2142 " --> pdb=" O LEU A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2145 through 2169 removed outlier: 3.714A pdb=" N VAL A2149 " --> pdb=" O SER A2145 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU A2150 " --> pdb=" O PRO A2146 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASP A2151 " --> pdb=" O SER A2147 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A2161 " --> pdb=" O GLU A2157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A2162 " --> pdb=" O CYS A2158 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A2166 " --> pdb=" O ILE A2162 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE A2167 " --> pdb=" O ARG A2163 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A2168 " --> pdb=" O SER A2164 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN A2169 " --> pdb=" O LEU A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2189 removed outlier: 5.450A pdb=" N LYS A2189 " --> pdb=" O ILE A2185 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2195 Proline residue: A2195 - end of helix Processing helix chain 'A' and resid 2196 through 2219 removed outlier: 3.637A pdb=" N GLY A2202 " --> pdb=" O MET A2198 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N MET A2203 " --> pdb=" O ARG A2199 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N HIS A2204 " --> pdb=" O ALA A2200 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU A2205 " --> pdb=" O LEU A2201 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A2214 " --> pdb=" O VAL A2210 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY A2218 " --> pdb=" O VAL A2214 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A2219 " --> pdb=" O LEU A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2225 through 2244 removed outlier: 3.915A pdb=" N VAL A2229 " --> pdb=" O PHE A2225 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A2241 " --> pdb=" O CYS A2237 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG A2244 " --> pdb=" O CYS A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2254 removed outlier: 4.347A pdb=" N HIS A2253 " --> pdb=" O SER A2249 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A2254 " --> pdb=" O MET A2250 " (cutoff:3.500A) Processing helix chain 'A' and resid 2255 through 2265 removed outlier: 3.916A pdb=" N GLY A2262 " --> pdb=" O LEU A2258 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE A2263 " --> pdb=" O GLU A2259 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A2264 " --> pdb=" O ASN A2260 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A2265 " --> pdb=" O SER A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2281 removed outlier: 3.687A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2308 Processing helix chain 'A' and resid 2310 through 2317 removed outlier: 3.728A pdb=" N GLY A2317 " --> pdb=" O LEU A2313 " (cutoff:3.500A) Processing helix chain 'A' and resid 2324 through 2340 removed outlier: 3.657A pdb=" N PHE A2334 " --> pdb=" O ARG A2330 " (cutoff:3.500A) Processing helix chain 'A' and resid 2346 through 2361 removed outlier: 3.566A pdb=" N ASN A2351 " --> pdb=" O GLU A2347 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Proline residue: A2361 - end of helix Processing helix chain 'A' and resid 2375 through 2390 Proline residue: A2390 - end of helix Processing helix chain 'A' and resid 2417 through 2437 Processing helix chain 'A' and resid 2439 through 2446 removed outlier: 3.854A pdb=" N ALA A2445 " --> pdb=" O HIS A2441 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY A2446 " --> pdb=" O LEU A2442 " (cutoff:3.500A) Processing helix chain 'A' and resid 2447 through 2462 Proline residue: A2462 - end of helix Processing helix chain 'A' and resid 2463 through 2472 Processing helix chain 'A' and resid 2495 through 2509 removed outlier: 3.972A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A2505 " --> pdb=" O SER A2501 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2525 removed outlier: 3.738A pdb=" N VAL A2524 " --> pdb=" O HIS A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2526 through 2538 removed outlier: 5.113A pdb=" N THR A2538 " --> pdb=" O ALA A2534 " (cutoff:3.500A) Processing helix chain 'A' and resid 2540 through 2545 removed outlier: 4.594A pdb=" N THR A2544 " --> pdb=" O THR A2540 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU A2545 " --> pdb=" O PHE A2541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2540 through 2545' Processing helix chain 'A' and resid 2546 through 2566 removed outlier: 5.513A pdb=" N LEU A2559 " --> pdb=" O CYS A2555 " (cutoff:3.500A) Proline residue: A2560 - end of helix Processing helix chain 'A' and resid 2575 through 2592 removed outlier: 3.700A pdb=" N VAL A2579 " --> pdb=" O ARG A2575 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A2592 " --> pdb=" O ARG A2588 " (cutoff:3.500A) Processing helix chain 'A' and resid 2596 through 2614 removed outlier: 4.088A pdb=" N VAL A2602 " --> pdb=" O ALA A2598 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A2603 " --> pdb=" O GLN A2599 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A2604 " --> pdb=" O ARG A2600 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A2613 " --> pdb=" O ALA A2609 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2630 removed outlier: 3.846A pdb=" N LEU A2619 " --> pdb=" O ARG A2615 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A2620 " --> pdb=" O PRO A2616 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS A2621 " --> pdb=" O SER A2617 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU A2622 " --> pdb=" O MET A2618 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A2628 " --> pdb=" O ARG A2624 " (cutoff:3.500A) Processing helix chain 'A' and resid 2637 through 2652 removed outlier: 3.544A pdb=" N LEU A2641 " --> pdb=" O ALA A2637 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A2642 " --> pdb=" O LYS A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2668 through 2690 removed outlier: 6.747A pdb=" N LEU A2672 " --> pdb=" O SER A2668 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A2673 " --> pdb=" O GLU A2669 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYS A2690 " --> pdb=" O LEU A2686 " (cutoff:3.500A) Processing helix chain 'A' and resid 2693 through 2711 removed outlier: 3.889A pdb=" N MET A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) Proline residue: A2701 - end of helix Proline residue: A2711 - end of helix Processing helix chain 'A' and resid 2748 through 2774 removed outlier: 4.978A pdb=" N ASP A2752 " --> pdb=" O PRO A2748 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER A2753 " --> pdb=" O GLU A2749 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE A2754 " --> pdb=" O LYS A2750 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A2757 " --> pdb=" O SER A2753 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN A2774 " --> pdb=" O LYS A2770 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2820 removed outlier: 4.314A pdb=" N LYS A2802 " --> pdb=" O SER A2798 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A2806 " --> pdb=" O LYS A2802 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TRP A2807 " --> pdb=" O GLU A2803 " (cutoff:3.500A) Proline residue: A2808 - end of helix removed outlier: 3.747A pdb=" N ALA A2818 " --> pdb=" O LYS A2814 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TRP A2819 " --> pdb=" O ALA A2815 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU A2820 " --> pdb=" O MET A2816 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2895 removed outlier: 4.626A pdb=" N GLU A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2934 removed outlier: 4.985A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A2922 " --> pdb=" O ARG A2918 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A2933 " --> pdb=" O PHE A2929 " (cutoff:3.500A) Processing helix chain 'A' and resid 2949 through 2954 removed outlier: 3.781A pdb=" N ARG A2954 " --> pdb=" O SER A2950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2955 through 2982 removed outlier: 4.332A pdb=" N ILE A2969 " --> pdb=" O ARG A2965 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A2976 " --> pdb=" O GLU A2972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3014 removed outlier: 4.866A pdb=" N LEU A3003 " --> pdb=" O ALA A2999 " (cutoff:3.500A) Proline residue: A3004 - end of helix Processing helix chain 'A' and resid 3032 through 3051 removed outlier: 3.897A pdb=" N THR A3040 " --> pdb=" O LYS A3036 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER A3041 " --> pdb=" O GLU A3037 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A3047 " --> pdb=" O PHE A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3053 through 3058 removed outlier: 3.862A pdb=" N PHE A3057 " --> pdb=" O ARG A3053 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY A3058 " --> pdb=" O VAL A3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3053 through 3058' Processing helix chain 'A' and resid 3060 through 3075 Processing helix chain 'A' and resid 3076 through 3083 Processing helix chain 'A' and resid 3085 through 3112 removed outlier: 4.334A pdb=" N LEU A3112 " --> pdb=" O GLU A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3123 through 3151 removed outlier: 3.606A pdb=" N THR A3133 " --> pdb=" O LEU A3129 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A3137 " --> pdb=" O THR A3133 " (cutoff:3.500A) Proline residue: A3138 - end of helix removed outlier: 3.540A pdb=" N HIS A3150 " --> pdb=" O HIS A3146 " (cutoff:3.500A) Processing helix chain 'A' and resid 3159 through 3176 removed outlier: 4.854A pdb=" N VAL A3163 " --> pdb=" O ASP A3159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A3175 " --> pdb=" O SER A3171 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY A3176 " --> pdb=" O ILE A3172 " (cutoff:3.500A) Processing helix chain 'A' and resid 3180 through 3201 Proline residue: A3188 - end of helix removed outlier: 3.535A pdb=" N ARG A3196 " --> pdb=" O GLU A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3207 through 3212 removed outlier: 4.629A pdb=" N GLU A3212 " --> pdb=" O PRO A3208 " (cutoff:3.500A) Processing helix chain 'A' and resid 3217 through 3222 Processing helix chain 'A' and resid 3223 through 3231 removed outlier: 4.773A pdb=" N ARG A3227 " --> pdb=" O SER A3223 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA A3228 " --> pdb=" O PRO A3224 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A3229 " --> pdb=" O ARG A3225 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A3230 " --> pdb=" O GLU A3226 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLY A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3223 through 3231' Processing helix chain 'A' and resid 3235 through 3241 removed outlier: 4.009A pdb=" N MET A3239 " --> pdb=" O SER A3235 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N CYS A3240 " --> pdb=" O VAL A3236 " (cutoff:3.500A) Proline residue: A3241 - end of helix No H-bonds generated for 'chain 'A' and resid 3235 through 3241' Processing helix chain 'A' and resid 3245 through 3260 removed outlier: 3.859A pdb=" N SER A3259 " --> pdb=" O GLY A3255 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A3260 " --> pdb=" O LEU A3256 " (cutoff:3.500A) Processing helix chain 'A' and resid 3262 through 3267 Proline residue: A3267 - end of helix Processing helix chain 'A' and resid 3268 through 3288 removed outlier: 4.244A pdb=" N LEU A3274 " --> pdb=" O ILE A3270 " (cutoff:3.500A) Proline residue: A3275 - end of helix Proline residue: A3282 - end of helix removed outlier: 4.084A pdb=" N GLU A3286 " --> pdb=" O PRO A3282 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG A3287 " --> pdb=" O ARG A3283 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A3288 " --> pdb=" O TRP A3284 " (cutoff:3.500A) Processing helix chain 'A' and resid 3308 through 3327 removed outlier: 3.623A pdb=" N LEU A3312 " --> pdb=" O THR A3308 " (cutoff:3.500A) Processing helix chain 'A' and resid 3333 through 3347 removed outlier: 4.172A pdb=" N ARG A3337 " --> pdb=" O THR A3333 " (cutoff:3.500A) Proline residue: A3344 - end of helix removed outlier: 4.407A pdb=" N SER A3347 " --> pdb=" O GLN A3343 " (cutoff:3.500A) Processing helix chain 'A' and resid 3350 through 3383 removed outlier: 4.024A pdb=" N LEU A3354 " --> pdb=" O ARG A3350 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS A3355 " --> pdb=" O PRO A3351 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE A3359 " --> pdb=" O HIS A3355 " (cutoff:3.500A) Proline residue: A3360 - end of helix removed outlier: 3.873A pdb=" N GLU A3382 " --> pdb=" O GLN A3378 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA A3383 " --> pdb=" O LEU A3379 " (cutoff:3.500A) Processing helix chain 'A' and resid 3384 through 3420 removed outlier: 4.306A pdb=" N GLU A3388 " --> pdb=" O LYS A3384 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY A3390 " --> pdb=" O GLU A3386 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A3392 " --> pdb=" O GLU A3388 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A3393 " --> pdb=" O GLU A3389 " (cutoff:3.500A) Proline residue: A3410 - end of helix removed outlier: 3.575A pdb=" N ASN A3418 " --> pdb=" O ARG A3414 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3427 Proline residue: A3427 - end of helix Processing helix chain 'A' and resid 3428 through 3449 removed outlier: 4.818A pdb=" N HIS A3449 " --> pdb=" O TRP A3445 " (cutoff:3.500A) Processing helix chain 'A' and resid 3450 through 3463 removed outlier: 3.606A pdb=" N GLN A3461 " --> pdb=" O ASN A3457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A3462 " --> pdb=" O PHE A3458 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3478 removed outlier: 6.759A pdb=" N PHE A3469 " --> pdb=" O ASN A3465 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU A3470 " --> pdb=" O ASN A3466 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP A3473 " --> pdb=" O PHE A3469 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER A3474 " --> pdb=" O LEU A3470 " (cutoff:3.500A) Processing helix chain 'A' and resid 3508 through 3526 removed outlier: 3.567A pdb=" N LEU A3514 " --> pdb=" O ILE A3510 " (cutoff:3.500A) Proline residue: A3519 - end of helix removed outlier: 3.705A pdb=" N MET A3524 " --> pdb=" O ILE A3520 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS A3525 " --> pdb=" O GLY A3521 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA A3526 " --> pdb=" O LEU A3522 " (cutoff:3.500A) Processing helix chain 'A' and resid 3527 through 3543 removed outlier: 5.222A pdb=" N ASP A3531 " --> pdb=" O PRO A3527 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A3532 " --> pdb=" O THR A3528 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A3537 " --> pdb=" O ILE A3533 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A3538 " --> pdb=" O MET A3534 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A3543 " --> pdb=" O ARG A3539 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3557 Processing helix chain 'A' and resid 3562 through 3567 removed outlier: 3.673A pdb=" N SER A3566 " --> pdb=" O LYS A3562 " (cutoff:3.500A) Proline residue: A3567 - end of helix No H-bonds generated for 'chain 'A' and resid 3562 through 3567' Processing helix chain 'A' and resid 3568 through 3580 removed outlier: 3.735A pdb=" N GLN A3572 " --> pdb=" O SER A3568 " (cutoff:3.500A) Proline residue: A3580 - end of helix Processing helix chain 'A' and resid 3588 through 3612 removed outlier: 3.702A pdb=" N ARG A3594 " --> pdb=" O GLU A3590 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A3607 " --> pdb=" O LEU A3603 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A3608 " --> pdb=" O TYR A3604 " (cutoff:3.500A) Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3628 through 3638 removed outlier: 3.877A pdb=" N VAL A3632 " --> pdb=" O ARG A3628 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A3636 " --> pdb=" O VAL A3632 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A3637 " --> pdb=" O VAL A3633 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3665 removed outlier: 3.690A pdb=" N GLU A3655 " --> pdb=" O ASN A3651 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU A3663 " --> pdb=" O ALA A3659 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR A3664 " --> pdb=" O ALA A3660 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3679 removed outlier: 3.757A pdb=" N LYS A3679 " --> pdb=" O ASP A3675 " (cutoff:3.500A) Processing helix chain 'A' and resid 3696 through 3711 removed outlier: 3.546A pdb=" N VAL A3702 " --> pdb=" O LEU A3698 " (cutoff:3.500A) Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 4.128A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N HIS A3734 " --> pdb=" O ALA A3730 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A3735 " --> pdb=" O LYS A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 removed outlier: 4.678A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A3759 " --> pdb=" O GLU A3755 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A3760 " --> pdb=" O LYS A3756 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A3770 " --> pdb=" O GLN A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 4.486A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3826 through 3839 Processing helix chain 'A' and resid 3843 through 3857 Processing helix chain 'A' and resid 3877 through 3893 Processing helix chain 'A' and resid 3896 through 3905 Processing helix chain 'A' and resid 3914 through 3939 removed outlier: 3.766A pdb=" N TYR A3937 " --> pdb=" O PHE A3933 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY A3939 " --> pdb=" O TRP A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3970 Processing helix chain 'A' and resid 3973 through 3983 Processing helix chain 'A' and resid 3984 through 4007 removed outlier: 3.799A pdb=" N ALA A3988 " --> pdb=" O ARG A3984 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP A4006 " --> pdb=" O LYS A4002 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N SER A4007 " --> pdb=" O LEU A4003 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.729A pdb=" N LEU A4019 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A4020 " --> pdb=" O LEU A4016 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A4032 " --> pdb=" O LEU A4028 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4052 Processing helix chain 'A' and resid 4053 through 4072 removed outlier: 3.792A pdb=" N MET A4064 " --> pdb=" O LYS A4060 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS A4069 " --> pdb=" O PHE A4065 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4082 removed outlier: 5.007A pdb=" N THR A4082 " --> pdb=" O GLN A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4101 removed outlier: 3.579A pdb=" N MET A4097 " --> pdb=" O PHE A4093 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP A4098 " --> pdb=" O GLN A4094 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER A4099 " --> pdb=" O LYS A4095 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN A4100 " --> pdb=" O ALA A4096 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A4101 " --> pdb=" O MET A4097 " (cutoff:3.500A) Processing helix chain 'A' and resid 4104 through 4116 removed outlier: 5.474A pdb=" N GLU A4116 " --> pdb=" O LEU A4112 " (cutoff:3.500A) Processing helix chain 'A' and resid 4124 through 4134 removed outlier: 3.643A pdb=" N PHE A4128 " --> pdb=" O ASN A4124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A4129 " --> pdb=" O PHE A4125 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A4130 " --> pdb=" O GLU A4126 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE A4132 " --> pdb=" O PHE A4128 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLN A4133 " --> pdb=" O ALA A4129 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU A4134 " --> pdb=" O ASN A4130 " (cutoff:3.500A) Processing helix chain 'A' and resid 4135 through 4155 removed outlier: 3.892A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Proline residue: A4155 - end of helix Processing helix chain 'A' and resid 4157 through 4168 removed outlier: 3.738A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A4162 " --> pdb=" O PRO A4158 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A4163 " --> pdb=" O ARG A4159 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A4164 " --> pdb=" O LEU A4160 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A4165 " --> pdb=" O ARG A4161 " (cutoff:3.500A) Processing helix chain 'A' and resid 4169 through 4176 removed outlier: 3.663A pdb=" N TYR A4173 " --> pdb=" O SER A4169 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A4174 " --> pdb=" O ILE A4170 " (cutoff:3.500A) Proline residue: A4176 - end of helix Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4208 through 4224 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4540 through 4559 Processing helix chain 'A' and resid 4560 through 4580 removed outlier: 3.752A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TYR A4580 " --> pdb=" O ILE A4576 " (cutoff:3.500A) Processing helix chain 'A' and resid 4640 through 4683 removed outlier: 3.599A pdb=" N ILE A4658 " --> pdb=" O ALA A4654 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A4666 " --> pdb=" O ASN A4662 " (cutoff:3.500A) Proline residue: A4667 - end of helix Processing helix chain 'A' and resid 4696 through 4709 removed outlier: 4.394A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A4708 " --> pdb=" O LEU A4704 " (cutoff:3.500A) Proline residue: A4709 - end of helix Processing helix chain 'A' and resid 4719 through 4729 Processing helix chain 'A' and resid 4733 through 4742 removed outlier: 4.142A pdb=" N ILE A4737 " --> pdb=" O GLY A4733 " (cutoff:3.500A) Processing helix chain 'A' and resid 4744 through 4750 removed outlier: 4.108A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A4750 " --> pdb=" O ALA A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4772 through 4786 Processing helix chain 'A' and resid 4787 through 4805 removed outlier: 4.043A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4808 through 4820 removed outlier: 5.032A pdb=" N HIS A4812 " --> pdb=" O PHE A4808 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A4813 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU A4814 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP A4815 " --> pdb=" O ALA A4811 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE A4816 " --> pdb=" O HIS A4812 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA A4817 " --> pdb=" O LEU A4813 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.871A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4858 Processing helix chain 'A' and resid 4859 through 4864 removed outlier: 4.272A pdb=" N TYR A4863 " --> pdb=" O PHE A4859 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN A4864 " --> pdb=" O ARG A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4859 through 4864' Processing helix chain 'A' and resid 4878 through 4893 removed outlier: 4.369A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4896 through 4901 removed outlier: 4.471A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4924 Processing helix chain 'A' and resid 4928 through 4957 removed outlier: 4.505A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 3.998A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 4999 through 5004 removed outlier: 3.817A pdb=" N HIS A5003 " --> pdb=" O ASP A4999 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THR A5004 " --> pdb=" O GLU A5000 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4999 through 5004' Processing helix chain 'A' and resid 5005 through 5017 Processing helix chain 'A' and resid 5027 through 5033 Processing helix chain 'B' and resid 61 through 66 removed outlier: 4.220A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 66' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.520A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.928A pdb=" N ALA B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.756A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 423 removed outlier: 3.694A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLY B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 Processing helix chain 'B' and resid 461 through 482 removed outlier: 3.762A pdb=" N GLN B 465 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 removed outlier: 3.519A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.086A pdb=" N TYR B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 removed outlier: 4.520A pdb=" N LYS B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 544 removed outlier: 3.863A pdb=" N PHE B 540 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 551 removed outlier: 3.759A pdb=" N LYS B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 4.240A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 567 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 570 " --> pdb=" O CYS B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 579 removed outlier: 3.998A pdb=" N ASN B 576 " --> pdb=" O PRO B 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 572 through 579' Processing helix chain 'B' and resid 580 through 593 removed outlier: 3.775A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 4.053A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 608 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 629 removed outlier: 4.242A pdb=" N LEU B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) Proline residue: B 627 - end of helix Processing helix chain 'B' and resid 810 through 815 removed outlier: 4.679A pdb=" N ALA B 814 " --> pdb=" O PRO B 810 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 815' Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.952A pdb=" N PHE B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 852 " --> pdb=" O HIS B 848 " (cutoff:3.500A) Proline residue: B 853 - end of helix No H-bonds generated for 'chain 'B' and resid 847 through 853' Processing helix chain 'B' and resid 864 through 885 removed outlier: 3.532A pdb=" N ILE B 870 " --> pdb=" O HIS B 866 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 878 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU B 880 " --> pdb=" O GLU B 876 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 881 " --> pdb=" O ASN B 877 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TRP B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA B 883 " --> pdb=" O HIS B 879 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.812A pdb=" N LEU B 913 " --> pdb=" O ASN B 909 " (cutoff:3.500A) Proline residue: B 914 - end of helix No H-bonds generated for 'chain 'B' and resid 909 through 914' Processing helix chain 'B' and resid 915 through 936 Processing helix chain 'B' and resid 945 through 950 removed outlier: 3.920A pdb=" N ASN B 949 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 1004 removed outlier: 3.524A pdb=" N VAL B 995 " --> pdb=" O ASN B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1048 removed outlier: 4.041A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1072 removed outlier: 4.635A pdb=" N ARG B1071 " --> pdb=" O SER B1067 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL B1072 " --> pdb=" O ARG B1068 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1067 through 1072' Processing helix chain 'B' and resid 1207 through 1212 removed outlier: 3.942A pdb=" N LEU B1211 " --> pdb=" O ASP B1207 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ARG B1212 " --> pdb=" O VAL B1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1207 through 1212' Processing helix chain 'B' and resid 1213 through 1218 removed outlier: 3.727A pdb=" N GLY B1218 " --> pdb=" O PHE B1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 1423 through 1430 removed outlier: 3.584A pdb=" N LEU B1428 " --> pdb=" O PRO B1424 " (cutoff:3.500A) Processing helix chain 'B' and resid 1444 through 1449 removed outlier: 3.933A pdb=" N VAL B1448 " --> pdb=" O GLU B1444 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TRP B1449 " --> pdb=" O PRO B1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1444 through 1449' Processing helix chain 'B' and resid 1496 through 1501 removed outlier: 4.588A pdb=" N PHE B1500 " --> pdb=" O TRP B1496 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B1501 " --> pdb=" O GLY B1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1496 through 1501' Processing helix chain 'B' and resid 1574 through 1581 removed outlier: 3.801A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B1580 " --> pdb=" O SER B1576 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1649 through 1657 removed outlier: 4.259A pdb=" N LEU B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B1654 " --> pdb=" O ILE B1650 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU B1655 " --> pdb=" O LEU B1651 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B1657 " --> pdb=" O LEU B1653 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 3.759A pdb=" N PHE B1662 " --> pdb=" O ASP B1658 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS B1674 " --> pdb=" O TYR B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1689 removed outlier: 3.530A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1700 removed outlier: 3.624A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1719 Processing helix chain 'B' and resid 1720 through 1734 removed outlier: 3.992A pdb=" N SER B1732 " --> pdb=" O ARG B1728 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU B1733 " --> pdb=" O SER B1729 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR B1734 " --> pdb=" O MET B1730 " (cutoff:3.500A) Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.836A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1825 removed outlier: 3.641A pdb=" N HIS B1825 " --> pdb=" O ASP B1821 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix Processing helix chain 'B' and resid 1855 through 1867 Processing helix chain 'B' and resid 1925 through 1930 removed outlier: 4.324A pdb=" N MET B1929 " --> pdb=" O GLY B1925 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS B1930 " --> pdb=" O LEU B1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1925 through 1930' Processing helix chain 'B' and resid 1934 through 1987 removed outlier: 3.828A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B1945 " --> pdb=" O ASN B1941 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B1982 " --> pdb=" O ALA B1978 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE B1984 " --> pdb=" O LEU B1980 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR B1985 " --> pdb=" O MET B1981 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET B1986 " --> pdb=" O ARG B1982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1990 through 2000 removed outlier: 4.256A pdb=" N ARG B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2011 removed outlier: 3.697A pdb=" N ASN B2007 " --> pdb=" O GLN B2003 " (cutoff:3.500A) Processing helix chain 'B' and resid 2017 through 2022 removed outlier: 3.540A pdb=" N CYS B2021 " --> pdb=" O ASP B2017 " (cutoff:3.500A) Proline residue: B2022 - end of helix No H-bonds generated for 'chain 'B' and resid 2017 through 2022' Processing helix chain 'B' and resid 2024 through 2043 Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.612A pdb=" N SER B2099 " --> pdb=" O GLN B2095 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 4.114A pdb=" N GLY B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2142 Proline residue: B2139 - end of helix removed outlier: 5.390A pdb=" N TYR B2142 " --> pdb=" O LEU B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2145 through 2169 removed outlier: 3.714A pdb=" N VAL B2149 " --> pdb=" O SER B2145 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU B2150 " --> pdb=" O PRO B2146 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASP B2151 " --> pdb=" O SER B2147 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B2161 " --> pdb=" O GLU B2157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B2162 " --> pdb=" O CYS B2158 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B2166 " --> pdb=" O ILE B2162 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE B2167 " --> pdb=" O ARG B2163 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL B2168 " --> pdb=" O SER B2164 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLN B2169 " --> pdb=" O LEU B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2189 removed outlier: 5.450A pdb=" N LYS B2189 " --> pdb=" O ILE B2185 " (cutoff:3.500A) Processing helix chain 'B' and resid 2190 through 2195 Proline residue: B2195 - end of helix Processing helix chain 'B' and resid 2196 through 2219 removed outlier: 3.638A pdb=" N GLY B2202 " --> pdb=" O MET B2198 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N MET B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N HIS B2204 " --> pdb=" O ALA B2200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU B2205 " --> pdb=" O LEU B2201 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B2214 " --> pdb=" O VAL B2210 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY B2218 " --> pdb=" O VAL B2214 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B2219 " --> pdb=" O LEU B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2225 through 2244 removed outlier: 3.915A pdb=" N VAL B2229 " --> pdb=" O PHE B2225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B2241 " --> pdb=" O CYS B2237 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG B2244 " --> pdb=" O CYS B2240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2254 removed outlier: 4.346A pdb=" N HIS B2253 " --> pdb=" O SER B2249 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B2254 " --> pdb=" O MET B2250 " (cutoff:3.500A) Processing helix chain 'B' and resid 2255 through 2265 removed outlier: 3.916A pdb=" N GLY B2262 " --> pdb=" O LEU B2258 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE B2263 " --> pdb=" O GLU B2259 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY B2264 " --> pdb=" O ASN B2260 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU B2265 " --> pdb=" O SER B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2281 removed outlier: 3.687A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2291 through 2308 Processing helix chain 'B' and resid 2310 through 2317 removed outlier: 3.727A pdb=" N GLY B2317 " --> pdb=" O LEU B2313 " (cutoff:3.500A) Processing helix chain 'B' and resid 2324 through 2340 removed outlier: 3.657A pdb=" N PHE B2334 " --> pdb=" O ARG B2330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2346 through 2361 removed outlier: 3.567A pdb=" N ASN B2351 " --> pdb=" O GLU B2347 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B2360 " --> pdb=" O LEU B2356 " (cutoff:3.500A) Proline residue: B2361 - end of helix Processing helix chain 'B' and resid 2375 through 2390 Proline residue: B2390 - end of helix Processing helix chain 'B' and resid 2417 through 2437 Processing helix chain 'B' and resid 2439 through 2446 removed outlier: 3.853A pdb=" N ALA B2445 " --> pdb=" O HIS B2441 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B2446 " --> pdb=" O LEU B2442 " (cutoff:3.500A) Processing helix chain 'B' and resid 2447 through 2462 Proline residue: B2462 - end of helix Processing helix chain 'B' and resid 2463 through 2472 Processing helix chain 'B' and resid 2495 through 2509 removed outlier: 3.972A pdb=" N LYS B2499 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B2505 " --> pdb=" O SER B2501 " (cutoff:3.500A) Processing helix chain 'B' and resid 2514 through 2525 removed outlier: 3.737A pdb=" N VAL B2524 " --> pdb=" O HIS B2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 2526 through 2538 removed outlier: 5.113A pdb=" N THR B2538 " --> pdb=" O ALA B2534 " (cutoff:3.500A) Processing helix chain 'B' and resid 2540 through 2545 removed outlier: 4.593A pdb=" N THR B2544 " --> pdb=" O THR B2540 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU B2545 " --> pdb=" O PHE B2541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2540 through 2545' Processing helix chain 'B' and resid 2546 through 2566 removed outlier: 5.514A pdb=" N LEU B2559 " --> pdb=" O CYS B2555 " (cutoff:3.500A) Proline residue: B2560 - end of helix Processing helix chain 'B' and resid 2575 through 2592 removed outlier: 3.700A pdb=" N VAL B2579 " --> pdb=" O ARG B2575 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B2592 " --> pdb=" O ARG B2588 " (cutoff:3.500A) Processing helix chain 'B' and resid 2596 through 2614 removed outlier: 4.088A pdb=" N VAL B2602 " --> pdb=" O ALA B2598 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B2603 " --> pdb=" O GLN B2599 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B2604 " --> pdb=" O ARG B2600 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B2613 " --> pdb=" O ALA B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2630 removed outlier: 3.846A pdb=" N LEU B2619 " --> pdb=" O ARG B2615 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B2620 " --> pdb=" O PRO B2616 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS B2621 " --> pdb=" O SER B2617 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU B2622 " --> pdb=" O MET B2618 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B2628 " --> pdb=" O ARG B2624 " (cutoff:3.500A) Processing helix chain 'B' and resid 2637 through 2652 removed outlier: 3.543A pdb=" N LEU B2641 " --> pdb=" O ALA B2637 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B2642 " --> pdb=" O LYS B2638 " (cutoff:3.500A) Processing helix chain 'B' and resid 2668 through 2690 removed outlier: 6.747A pdb=" N LEU B2672 " --> pdb=" O SER B2668 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS B2673 " --> pdb=" O GLU B2669 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS B2690 " --> pdb=" O LEU B2686 " (cutoff:3.500A) Processing helix chain 'B' and resid 2693 through 2711 removed outlier: 3.889A pdb=" N MET B2698 " --> pdb=" O GLU B2694 " (cutoff:3.500A) Proline residue: B2701 - end of helix Proline residue: B2711 - end of helix Processing helix chain 'B' and resid 2748 through 2774 removed outlier: 4.978A pdb=" N ASP B2752 " --> pdb=" O PRO B2748 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER B2753 " --> pdb=" O GLU B2749 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE B2754 " --> pdb=" O LYS B2750 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B2757 " --> pdb=" O SER B2753 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN B2774 " --> pdb=" O LYS B2770 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2820 removed outlier: 4.314A pdb=" N LYS B2802 " --> pdb=" O SER B2798 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B2806 " --> pdb=" O LYS B2802 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TRP B2807 " --> pdb=" O GLU B2803 " (cutoff:3.500A) Proline residue: B2808 - end of helix removed outlier: 3.746A pdb=" N ALA B2818 " --> pdb=" O LYS B2814 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TRP B2819 " --> pdb=" O ALA B2815 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU B2820 " --> pdb=" O MET B2816 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.626A pdb=" N GLU B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2934 removed outlier: 4.983A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B2922 " --> pdb=" O ARG B2918 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B2933 " --> pdb=" O PHE B2929 " (cutoff:3.500A) Processing helix chain 'B' and resid 2949 through 2954 removed outlier: 3.780A pdb=" N ARG B2954 " --> pdb=" O SER B2950 " (cutoff:3.500A) Processing helix chain 'B' and resid 2955 through 2982 removed outlier: 4.331A pdb=" N ILE B2969 " --> pdb=" O ARG B2965 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA B2975 " --> pdb=" O GLN B2971 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS B2976 " --> pdb=" O GLU B2972 " (cutoff:3.500A) Processing helix chain 'B' and resid 2991 through 3014 removed outlier: 4.866A pdb=" N LEU B3003 " --> pdb=" O ALA B2999 " (cutoff:3.500A) Proline residue: B3004 - end of helix Processing helix chain 'B' and resid 3032 through 3051 removed outlier: 3.898A pdb=" N THR B3040 " --> pdb=" O LYS B3036 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B3041 " --> pdb=" O GLU B3037 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B3047 " --> pdb=" O PHE B3043 " (cutoff:3.500A) Processing helix chain 'B' and resid 3053 through 3058 removed outlier: 3.861A pdb=" N PHE B3057 " --> pdb=" O ARG B3053 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY B3058 " --> pdb=" O VAL B3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3053 through 3058' Processing helix chain 'B' and resid 3060 through 3075 Processing helix chain 'B' and resid 3076 through 3083 Processing helix chain 'B' and resid 3085 through 3112 removed outlier: 4.335A pdb=" N LEU B3112 " --> pdb=" O GLU B3108 " (cutoff:3.500A) Processing helix chain 'B' and resid 3123 through 3151 removed outlier: 3.607A pdb=" N THR B3133 " --> pdb=" O LEU B3129 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU B3137 " --> pdb=" O THR B3133 " (cutoff:3.500A) Proline residue: B3138 - end of helix removed outlier: 3.541A pdb=" N HIS B3150 " --> pdb=" O HIS B3146 " (cutoff:3.500A) Processing helix chain 'B' and resid 3159 through 3176 removed outlier: 4.854A pdb=" N VAL B3163 " --> pdb=" O ASP B3159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B3175 " --> pdb=" O SER B3171 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY B3176 " --> pdb=" O ILE B3172 " (cutoff:3.500A) Processing helix chain 'B' and resid 3180 through 3201 Proline residue: B3188 - end of helix removed outlier: 3.535A pdb=" N ARG B3196 " --> pdb=" O GLU B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3207 through 3212 removed outlier: 4.629A pdb=" N GLU B3212 " --> pdb=" O PRO B3208 " (cutoff:3.500A) Processing helix chain 'B' and resid 3217 through 3222 Processing helix chain 'B' and resid 3223 through 3231 removed outlier: 4.772A pdb=" N ARG B3227 " --> pdb=" O SER B3223 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA B3228 " --> pdb=" O PRO B3224 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE B3229 " --> pdb=" O ARG B3225 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B3230 " --> pdb=" O GLU B3226 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3223 through 3231' Processing helix chain 'B' and resid 3235 through 3241 removed outlier: 4.007A pdb=" N MET B3239 " --> pdb=" O SER B3235 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N CYS B3240 " --> pdb=" O VAL B3236 " (cutoff:3.500A) Proline residue: B3241 - end of helix No H-bonds generated for 'chain 'B' and resid 3235 through 3241' Processing helix chain 'B' and resid 3245 through 3260 removed outlier: 3.859A pdb=" N SER B3259 " --> pdb=" O GLY B3255 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B3260 " --> pdb=" O LEU B3256 " (cutoff:3.500A) Processing helix chain 'B' and resid 3262 through 3267 Proline residue: B3267 - end of helix Processing helix chain 'B' and resid 3268 through 3288 removed outlier: 4.245A pdb=" N LEU B3274 " --> pdb=" O ILE B3270 " (cutoff:3.500A) Proline residue: B3275 - end of helix Proline residue: B3282 - end of helix removed outlier: 4.084A pdb=" N GLU B3286 " --> pdb=" O PRO B3282 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG B3287 " --> pdb=" O ARG B3283 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B3288 " --> pdb=" O TRP B3284 " (cutoff:3.500A) Processing helix chain 'B' and resid 3308 through 3327 removed outlier: 3.622A pdb=" N LEU B3312 " --> pdb=" O THR B3308 " (cutoff:3.500A) Processing helix chain 'B' and resid 3333 through 3347 removed outlier: 4.171A pdb=" N ARG B3337 " --> pdb=" O THR B3333 " (cutoff:3.500A) Proline residue: B3344 - end of helix removed outlier: 4.407A pdb=" N SER B3347 " --> pdb=" O GLN B3343 " (cutoff:3.500A) Processing helix chain 'B' and resid 3350 through 3383 removed outlier: 4.024A pdb=" N LEU B3354 " --> pdb=" O ARG B3350 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS B3355 " --> pdb=" O PRO B3351 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE B3359 " --> pdb=" O HIS B3355 " (cutoff:3.500A) Proline residue: B3360 - end of helix removed outlier: 3.873A pdb=" N GLU B3382 " --> pdb=" O GLN B3378 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA B3383 " --> pdb=" O LEU B3379 " (cutoff:3.500A) Processing helix chain 'B' and resid 3384 through 3420 removed outlier: 4.307A pdb=" N GLU B3388 " --> pdb=" O LYS B3384 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY B3390 " --> pdb=" O GLU B3386 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B3392 " --> pdb=" O GLU B3388 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B3393 " --> pdb=" O GLU B3389 " (cutoff:3.500A) Proline residue: B3410 - end of helix removed outlier: 3.575A pdb=" N ASN B3418 " --> pdb=" O ARG B3414 " (cutoff:3.500A) Processing helix chain 'B' and resid 3421 through 3427 Proline residue: B3427 - end of helix Processing helix chain 'B' and resid 3428 through 3449 removed outlier: 4.818A pdb=" N HIS B3449 " --> pdb=" O TRP B3445 " (cutoff:3.500A) Processing helix chain 'B' and resid 3450 through 3463 removed outlier: 3.607A pdb=" N GLN B3461 " --> pdb=" O ASN B3457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B3462 " --> pdb=" O PHE B3458 " (cutoff:3.500A) Processing helix chain 'B' and resid 3465 through 3478 removed outlier: 6.759A pdb=" N PHE B3469 " --> pdb=" O ASN B3465 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU B3470 " --> pdb=" O ASN B3466 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP B3473 " --> pdb=" O PHE B3469 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER B3474 " --> pdb=" O LEU B3470 " (cutoff:3.500A) Processing helix chain 'B' and resid 3508 through 3526 removed outlier: 3.567A pdb=" N LEU B3514 " --> pdb=" O ILE B3510 " (cutoff:3.500A) Proline residue: B3519 - end of helix removed outlier: 3.705A pdb=" N MET B3524 " --> pdb=" O ILE B3520 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B3525 " --> pdb=" O GLY B3521 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA B3526 " --> pdb=" O LEU B3522 " (cutoff:3.500A) Processing helix chain 'B' and resid 3527 through 3543 removed outlier: 5.221A pdb=" N ASP B3531 " --> pdb=" O PRO B3527 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU B3532 " --> pdb=" O THR B3528 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B3537 " --> pdb=" O ILE B3533 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B3538 " --> pdb=" O MET B3534 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B3543 " --> pdb=" O ARG B3539 " (cutoff:3.500A) Processing helix chain 'B' and resid 3545 through 3557 Processing helix chain 'B' and resid 3562 through 3567 removed outlier: 3.673A pdb=" N SER B3566 " --> pdb=" O LYS B3562 " (cutoff:3.500A) Proline residue: B3567 - end of helix No H-bonds generated for 'chain 'B' and resid 3562 through 3567' Processing helix chain 'B' and resid 3568 through 3580 removed outlier: 3.734A pdb=" N GLN B3572 " --> pdb=" O SER B3568 " (cutoff:3.500A) Proline residue: B3580 - end of helix Processing helix chain 'B' and resid 3588 through 3612 removed outlier: 3.703A pdb=" N ARG B3594 " --> pdb=" O GLU B3590 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B3607 " --> pdb=" O LEU B3603 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B3608 " --> pdb=" O TYR B3604 " (cutoff:3.500A) Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3628 through 3638 removed outlier: 3.876A pdb=" N VAL B3632 " --> pdb=" O ARG B3628 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B3636 " --> pdb=" O VAL B3632 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG B3637 " --> pdb=" O VAL B3633 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3665 removed outlier: 3.690A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU B3663 " --> pdb=" O ALA B3659 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N THR B3664 " --> pdb=" O ALA B3660 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3679 removed outlier: 3.757A pdb=" N LYS B3679 " --> pdb=" O ASP B3675 " (cutoff:3.500A) Processing helix chain 'B' and resid 3696 through 3711 removed outlier: 3.546A pdb=" N VAL B3702 " --> pdb=" O LEU B3698 " (cutoff:3.500A) Processing helix chain 'B' and resid 3719 through 3735 removed outlier: 4.127A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N HIS B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B3735 " --> pdb=" O LYS B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3772 removed outlier: 4.678A pdb=" N MET B3758 " --> pdb=" O GLU B3754 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B3759 " --> pdb=" O GLU B3755 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS B3760 " --> pdb=" O LYS B3756 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B3770 " --> pdb=" O GLN B3766 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 4.485A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3826 through 3839 Processing helix chain 'B' and resid 3843 through 3857 Processing helix chain 'B' and resid 3877 through 3893 Processing helix chain 'B' and resid 3896 through 3905 Processing helix chain 'B' and resid 3914 through 3939 removed outlier: 3.766A pdb=" N TYR B3937 " --> pdb=" O PHE B3933 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B3939 " --> pdb=" O TRP B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3970 Processing helix chain 'B' and resid 3973 through 3983 Processing helix chain 'B' and resid 3984 through 4007 removed outlier: 3.799A pdb=" N ALA B3988 " --> pdb=" O ARG B3984 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP B4006 " --> pdb=" O LYS B4002 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER B4007 " --> pdb=" O LEU B4003 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.729A pdb=" N LEU B4019 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B4020 " --> pdb=" O LEU B4016 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B4032 " --> pdb=" O LEU B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4052 Processing helix chain 'B' and resid 4053 through 4072 removed outlier: 3.792A pdb=" N MET B4064 " --> pdb=" O LYS B4060 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B4069 " --> pdb=" O PHE B4065 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4082 removed outlier: 5.008A pdb=" N THR B4082 " --> pdb=" O GLN B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4101 removed outlier: 3.579A pdb=" N MET B4097 " --> pdb=" O PHE B4093 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER B4099 " --> pdb=" O LYS B4095 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN B4100 " --> pdb=" O ALA B4096 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B4101 " --> pdb=" O MET B4097 " (cutoff:3.500A) Processing helix chain 'B' and resid 4104 through 4116 removed outlier: 5.475A pdb=" N GLU B4116 " --> pdb=" O LEU B4112 " (cutoff:3.500A) Processing helix chain 'B' and resid 4124 through 4134 removed outlier: 3.643A pdb=" N PHE B4128 " --> pdb=" O ASN B4124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B4129 " --> pdb=" O PHE B4125 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B4130 " --> pdb=" O GLU B4126 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE B4132 " --> pdb=" O PHE B4128 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLN B4133 " --> pdb=" O ALA B4129 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU B4134 " --> pdb=" O ASN B4130 " (cutoff:3.500A) Processing helix chain 'B' and resid 4135 through 4155 removed outlier: 3.892A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) Proline residue: B4155 - end of helix Processing helix chain 'B' and resid 4157 through 4168 removed outlier: 3.739A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN B4162 " --> pdb=" O PRO B4158 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B4163 " --> pdb=" O ARG B4159 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B4164 " --> pdb=" O LEU B4160 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B4165 " --> pdb=" O ARG B4161 " (cutoff:3.500A) Processing helix chain 'B' and resid 4169 through 4176 removed outlier: 3.663A pdb=" N TYR B4173 " --> pdb=" O SER B4169 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B4174 " --> pdb=" O ILE B4170 " (cutoff:3.500A) Proline residue: B4176 - end of helix Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4208 through 4224 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4540 through 4559 Processing helix chain 'B' and resid 4560 through 4580 removed outlier: 3.752A pdb=" N LEU B4578 " --> pdb=" O ASN B4574 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR B4580 " --> pdb=" O ILE B4576 " (cutoff:3.500A) Processing helix chain 'B' and resid 4640 through 4683 removed outlier: 3.599A pdb=" N ILE B4658 " --> pdb=" O ALA B4654 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B4666 " --> pdb=" O ASN B4662 " (cutoff:3.500A) Proline residue: B4667 - end of helix Processing helix chain 'B' and resid 4696 through 4709 removed outlier: 4.394A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR B4708 " --> pdb=" O LEU B4704 " (cutoff:3.500A) Proline residue: B4709 - end of helix Processing helix chain 'B' and resid 4719 through 4729 Processing helix chain 'B' and resid 4733 through 4742 removed outlier: 4.143A pdb=" N ILE B4737 " --> pdb=" O GLY B4733 " (cutoff:3.500A) Processing helix chain 'B' and resid 4744 through 4750 removed outlier: 4.107A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B4750 " --> pdb=" O ALA B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4772 through 4786 Processing helix chain 'B' and resid 4787 through 4805 removed outlier: 4.043A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4808 through 4820 removed outlier: 5.031A pdb=" N HIS B4812 " --> pdb=" O PHE B4808 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU B4813 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU B4814 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP B4815 " --> pdb=" O ALA B4811 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B4816 " --> pdb=" O HIS B4812 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA B4817 " --> pdb=" O LEU B4813 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.872A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4858 Processing helix chain 'B' and resid 4859 through 4864 removed outlier: 4.272A pdb=" N TYR B4863 " --> pdb=" O PHE B4859 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASN B4864 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4859 through 4864' Processing helix chain 'B' and resid 4878 through 4893 removed outlier: 4.368A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4896 through 4901 removed outlier: 4.471A pdb=" N GLU B4900 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4924 Processing helix chain 'B' and resid 4928 through 4957 removed outlier: 4.506A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 3.997A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 4999 through 5004 removed outlier: 3.817A pdb=" N HIS B5003 " --> pdb=" O ASP B4999 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THR B5004 " --> pdb=" O GLU B5000 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4999 through 5004' Processing helix chain 'B' and resid 5005 through 5017 Processing helix chain 'B' and resid 5027 through 5033 Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.221A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 66' Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.519A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.928A pdb=" N ALA C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N HIS C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.757A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 423 removed outlier: 3.694A pdb=" N HIS C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 420 " --> pdb=" O LYS C 416 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 453 Processing helix chain 'C' and resid 461 through 482 removed outlier: 3.762A pdb=" N GLN C 465 " --> pdb=" O HIS C 461 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.518A pdb=" N LEU C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.085A pdb=" N TYR C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 531 removed outlier: 4.519A pdb=" N LYS C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 544 removed outlier: 3.863A pdb=" N PHE C 540 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 551 removed outlier: 3.758A pdb=" N LYS C 550 " --> pdb=" O TRP C 546 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 4.239A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 567 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 570 " --> pdb=" O CYS C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 579 removed outlier: 3.999A pdb=" N ASN C 576 " --> pdb=" O PRO C 572 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE C 577 " --> pdb=" O GLU C 573 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 572 through 579' Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.775A pdb=" N LEU C 590 " --> pdb=" O ILE C 586 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 591 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 4.052A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 608 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 629 removed outlier: 4.242A pdb=" N LEU C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) Proline residue: C 627 - end of helix Processing helix chain 'C' and resid 810 through 815 removed outlier: 4.679A pdb=" N ALA C 814 " --> pdb=" O PRO C 810 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL C 815 " --> pdb=" O CYS C 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 810 through 815' Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.951A pdb=" N PHE C 851 " --> pdb=" O SER C 847 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 852 " --> pdb=" O HIS C 848 " (cutoff:3.500A) Proline residue: C 853 - end of helix No H-bonds generated for 'chain 'C' and resid 847 through 853' Processing helix chain 'C' and resid 864 through 885 removed outlier: 3.532A pdb=" N ILE C 870 " --> pdb=" O HIS C 866 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS C 873 " --> pdb=" O ARG C 869 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE C 878 " --> pdb=" O LEU C 874 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU C 880 " --> pdb=" O GLU C 876 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N TRP C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA C 883 " --> pdb=" O HIS C 879 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.812A pdb=" N LEU C 913 " --> pdb=" O ASN C 909 " (cutoff:3.500A) Proline residue: C 914 - end of helix No H-bonds generated for 'chain 'C' and resid 909 through 914' Processing helix chain 'C' and resid 915 through 936 Processing helix chain 'C' and resid 945 through 950 removed outlier: 3.919A pdb=" N ASN C 949 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1004 removed outlier: 3.524A pdb=" N VAL C 995 " --> pdb=" O ASN C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1048 removed outlier: 4.042A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1072 removed outlier: 4.634A pdb=" N ARG C1071 " --> pdb=" O SER C1067 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL C1072 " --> pdb=" O ARG C1068 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1067 through 1072' Processing helix chain 'C' and resid 1207 through 1212 removed outlier: 3.941A pdb=" N LEU C1211 " --> pdb=" O ASP C1207 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ARG C1212 " --> pdb=" O VAL C1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1207 through 1212' Processing helix chain 'C' and resid 1213 through 1218 removed outlier: 3.728A pdb=" N GLY C1218 " --> pdb=" O PHE C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1423 through 1430 removed outlier: 3.583A pdb=" N LEU C1428 " --> pdb=" O PRO C1424 " (cutoff:3.500A) Processing helix chain 'C' and resid 1444 through 1449 removed outlier: 3.932A pdb=" N VAL C1448 " --> pdb=" O GLU C1444 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TRP C1449 " --> pdb=" O PRO C1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1444 through 1449' Processing helix chain 'C' and resid 1496 through 1501 removed outlier: 4.588A pdb=" N PHE C1500 " --> pdb=" O TRP C1496 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C1501 " --> pdb=" O GLY C1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1496 through 1501' Processing helix chain 'C' and resid 1574 through 1581 removed outlier: 3.801A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE C1580 " --> pdb=" O SER C1576 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU C1581 " --> pdb=" O ALA C1577 " (cutoff:3.500A) Processing helix chain 'C' and resid 1649 through 1657 removed outlier: 4.260A pdb=" N LEU C1653 " --> pdb=" O ASP C1649 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER C1654 " --> pdb=" O ILE C1650 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU C1655 " --> pdb=" O LEU C1651 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C1657 " --> pdb=" O LEU C1653 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 3.759A pdb=" N PHE C1662 " --> pdb=" O ASP C1658 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS C1674 " --> pdb=" O TYR C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1689 removed outlier: 3.530A pdb=" N CYS C1686 " --> pdb=" O ALA C1682 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1700 removed outlier: 3.623A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1719 Processing helix chain 'C' and resid 1720 through 1734 removed outlier: 3.992A pdb=" N SER C1732 " --> pdb=" O ARG C1728 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU C1733 " --> pdb=" O SER C1729 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR C1734 " --> pdb=" O MET C1730 " (cutoff:3.500A) Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.836A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1825 removed outlier: 3.642A pdb=" N HIS C1825 " --> pdb=" O ASP C1821 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1855 through 1867 Processing helix chain 'C' and resid 1925 through 1930 removed outlier: 4.324A pdb=" N MET C1929 " --> pdb=" O GLY C1925 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS C1930 " --> pdb=" O LEU C1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1925 through 1930' Processing helix chain 'C' and resid 1934 through 1987 removed outlier: 3.828A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C1945 " --> pdb=" O ASN C1941 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP C1967 " --> pdb=" O GLU C1963 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C1982 " --> pdb=" O ALA C1978 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE C1984 " --> pdb=" O LEU C1980 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR C1985 " --> pdb=" O MET C1981 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET C1986 " --> pdb=" O ARG C1982 " (cutoff:3.500A) Processing helix chain 'C' and resid 1990 through 2000 removed outlier: 4.256A pdb=" N ARG C1994 " --> pdb=" O GLU C1990 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU C1997 " --> pdb=" O ARG C1993 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2001 through 2011 removed outlier: 3.697A pdb=" N ASN C2007 " --> pdb=" O GLN C2003 " (cutoff:3.500A) Processing helix chain 'C' and resid 2017 through 2022 removed outlier: 3.539A pdb=" N CYS C2021 " --> pdb=" O ASP C2017 " (cutoff:3.500A) Proline residue: C2022 - end of helix No H-bonds generated for 'chain 'C' and resid 2017 through 2022' Processing helix chain 'C' and resid 2024 through 2043 Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.612A pdb=" N SER C2099 " --> pdb=" O GLN C2095 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 4.114A pdb=" N GLY C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2142 Proline residue: C2139 - end of helix removed outlier: 5.391A pdb=" N TYR C2142 " --> pdb=" O LEU C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2145 through 2169 removed outlier: 3.713A pdb=" N VAL C2149 " --> pdb=" O SER C2145 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU C2150 " --> pdb=" O PRO C2146 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASP C2151 " --> pdb=" O SER C2147 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C2161 " --> pdb=" O GLU C2157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C2162 " --> pdb=" O CYS C2158 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C2166 " --> pdb=" O ILE C2162 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C2167 " --> pdb=" O ARG C2163 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL C2168 " --> pdb=" O SER C2164 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN C2169 " --> pdb=" O LEU C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2171 through 2189 removed outlier: 5.448A pdb=" N LYS C2189 " --> pdb=" O ILE C2185 " (cutoff:3.500A) Processing helix chain 'C' and resid 2190 through 2195 Proline residue: C2195 - end of helix Processing helix chain 'C' and resid 2196 through 2219 removed outlier: 3.638A pdb=" N GLY C2202 " --> pdb=" O MET C2198 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N MET C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N HIS C2204 " --> pdb=" O ALA C2200 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU C2205 " --> pdb=" O LEU C2201 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C2214 " --> pdb=" O VAL C2210 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY C2218 " --> pdb=" O VAL C2214 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C2219 " --> pdb=" O LEU C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2244 removed outlier: 3.914A pdb=" N VAL C2229 " --> pdb=" O PHE C2225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C2241 " --> pdb=" O CYS C2237 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG C2244 " --> pdb=" O CYS C2240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2245 through 2254 removed outlier: 4.347A pdb=" N HIS C2253 " --> pdb=" O SER C2249 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C2254 " --> pdb=" O MET C2250 " (cutoff:3.500A) Processing helix chain 'C' and resid 2255 through 2265 removed outlier: 3.916A pdb=" N GLY C2262 " --> pdb=" O LEU C2258 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE C2263 " --> pdb=" O GLU C2259 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY C2264 " --> pdb=" O ASN C2260 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU C2265 " --> pdb=" O SER C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2281 removed outlier: 3.687A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) Processing helix chain 'C' and resid 2291 through 2308 Processing helix chain 'C' and resid 2310 through 2317 removed outlier: 3.727A pdb=" N GLY C2317 " --> pdb=" O LEU C2313 " (cutoff:3.500A) Processing helix chain 'C' and resid 2324 through 2340 removed outlier: 3.657A pdb=" N PHE C2334 " --> pdb=" O ARG C2330 " (cutoff:3.500A) Processing helix chain 'C' and resid 2346 through 2361 removed outlier: 3.567A pdb=" N ASN C2351 " --> pdb=" O GLU C2347 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Proline residue: C2361 - end of helix Processing helix chain 'C' and resid 2375 through 2390 Proline residue: C2390 - end of helix Processing helix chain 'C' and resid 2417 through 2437 Processing helix chain 'C' and resid 2439 through 2446 removed outlier: 3.853A pdb=" N ALA C2445 " --> pdb=" O HIS C2441 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C2446 " --> pdb=" O LEU C2442 " (cutoff:3.500A) Processing helix chain 'C' and resid 2447 through 2462 Proline residue: C2462 - end of helix Processing helix chain 'C' and resid 2463 through 2472 Processing helix chain 'C' and resid 2495 through 2509 removed outlier: 3.972A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C2505 " --> pdb=" O SER C2501 " (cutoff:3.500A) Processing helix chain 'C' and resid 2514 through 2525 removed outlier: 3.737A pdb=" N VAL C2524 " --> pdb=" O HIS C2520 " (cutoff:3.500A) Processing helix chain 'C' and resid 2526 through 2538 removed outlier: 5.112A pdb=" N THR C2538 " --> pdb=" O ALA C2534 " (cutoff:3.500A) Processing helix chain 'C' and resid 2540 through 2545 removed outlier: 4.593A pdb=" N THR C2544 " --> pdb=" O THR C2540 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU C2545 " --> pdb=" O PHE C2541 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2540 through 2545' Processing helix chain 'C' and resid 2546 through 2566 removed outlier: 5.514A pdb=" N LEU C2559 " --> pdb=" O CYS C2555 " (cutoff:3.500A) Proline residue: C2560 - end of helix Processing helix chain 'C' and resid 2575 through 2592 removed outlier: 3.700A pdb=" N VAL C2579 " --> pdb=" O ARG C2575 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C2592 " --> pdb=" O ARG C2588 " (cutoff:3.500A) Processing helix chain 'C' and resid 2596 through 2614 removed outlier: 4.088A pdb=" N VAL C2602 " --> pdb=" O ALA C2598 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C2603 " --> pdb=" O GLN C2599 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C2604 " --> pdb=" O ARG C2600 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR C2613 " --> pdb=" O ALA C2609 " (cutoff:3.500A) Processing helix chain 'C' and resid 2615 through 2630 removed outlier: 3.846A pdb=" N LEU C2619 " --> pdb=" O ARG C2615 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C2620 " --> pdb=" O PRO C2616 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS C2621 " --> pdb=" O SER C2617 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU C2622 " --> pdb=" O MET C2618 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE C2628 " --> pdb=" O ARG C2624 " (cutoff:3.500A) Processing helix chain 'C' and resid 2637 through 2652 removed outlier: 3.543A pdb=" N LEU C2641 " --> pdb=" O ALA C2637 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C2642 " --> pdb=" O LYS C2638 " (cutoff:3.500A) Processing helix chain 'C' and resid 2668 through 2690 removed outlier: 6.747A pdb=" N LEU C2672 " --> pdb=" O SER C2668 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS C2673 " --> pdb=" O GLU C2669 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS C2690 " --> pdb=" O LEU C2686 " (cutoff:3.500A) Processing helix chain 'C' and resid 2693 through 2711 removed outlier: 3.889A pdb=" N MET C2698 " --> pdb=" O GLU C2694 " (cutoff:3.500A) Proline residue: C2701 - end of helix Proline residue: C2711 - end of helix Processing helix chain 'C' and resid 2748 through 2774 removed outlier: 4.978A pdb=" N ASP C2752 " --> pdb=" O PRO C2748 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER C2753 " --> pdb=" O GLU C2749 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE C2754 " --> pdb=" O LYS C2750 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C2757 " --> pdb=" O SER C2753 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN C2774 " --> pdb=" O LYS C2770 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2820 removed outlier: 4.314A pdb=" N LYS C2802 " --> pdb=" O SER C2798 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG C2806 " --> pdb=" O LYS C2802 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TRP C2807 " --> pdb=" O GLU C2803 " (cutoff:3.500A) Proline residue: C2808 - end of helix removed outlier: 3.747A pdb=" N ALA C2818 " --> pdb=" O LYS C2814 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TRP C2819 " --> pdb=" O ALA C2815 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU C2820 " --> pdb=" O MET C2816 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2895 removed outlier: 4.626A pdb=" N GLU C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2934 removed outlier: 4.984A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C2922 " --> pdb=" O ARG C2918 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C2933 " --> pdb=" O PHE C2929 " (cutoff:3.500A) Processing helix chain 'C' and resid 2949 through 2954 removed outlier: 3.782A pdb=" N ARG C2954 " --> pdb=" O SER C2950 " (cutoff:3.500A) Processing helix chain 'C' and resid 2955 through 2982 removed outlier: 4.333A pdb=" N ILE C2969 " --> pdb=" O ARG C2965 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA C2975 " --> pdb=" O GLN C2971 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS C2976 " --> pdb=" O GLU C2972 " (cutoff:3.500A) Processing helix chain 'C' and resid 2991 through 3014 removed outlier: 4.866A pdb=" N LEU C3003 " --> pdb=" O ALA C2999 " (cutoff:3.500A) Proline residue: C3004 - end of helix Processing helix chain 'C' and resid 3032 through 3051 removed outlier: 3.898A pdb=" N THR C3040 " --> pdb=" O LYS C3036 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C3041 " --> pdb=" O GLU C3037 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C3047 " --> pdb=" O PHE C3043 " (cutoff:3.500A) Processing helix chain 'C' and resid 3053 through 3058 removed outlier: 3.862A pdb=" N PHE C3057 " --> pdb=" O ARG C3053 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY C3058 " --> pdb=" O VAL C3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3053 through 3058' Processing helix chain 'C' and resid 3060 through 3075 Processing helix chain 'C' and resid 3076 through 3083 Processing helix chain 'C' and resid 3085 through 3112 removed outlier: 4.335A pdb=" N LEU C3112 " --> pdb=" O GLU C3108 " (cutoff:3.500A) Processing helix chain 'C' and resid 3123 through 3151 removed outlier: 3.607A pdb=" N THR C3133 " --> pdb=" O LEU C3129 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU C3137 " --> pdb=" O THR C3133 " (cutoff:3.500A) Proline residue: C3138 - end of helix removed outlier: 3.540A pdb=" N HIS C3150 " --> pdb=" O HIS C3146 " (cutoff:3.500A) Processing helix chain 'C' and resid 3159 through 3176 removed outlier: 4.854A pdb=" N VAL C3163 " --> pdb=" O ASP C3159 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C3175 " --> pdb=" O SER C3171 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY C3176 " --> pdb=" O ILE C3172 " (cutoff:3.500A) Processing helix chain 'C' and resid 3180 through 3201 Proline residue: C3188 - end of helix removed outlier: 3.535A pdb=" N ARG C3196 " --> pdb=" O GLU C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3207 through 3212 removed outlier: 4.629A pdb=" N GLU C3212 " --> pdb=" O PRO C3208 " (cutoff:3.500A) Processing helix chain 'C' and resid 3217 through 3222 Processing helix chain 'C' and resid 3223 through 3231 removed outlier: 4.772A pdb=" N ARG C3227 " --> pdb=" O SER C3223 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA C3228 " --> pdb=" O PRO C3224 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE C3229 " --> pdb=" O ARG C3225 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C3230 " --> pdb=" O GLU C3226 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3223 through 3231' Processing helix chain 'C' and resid 3235 through 3241 removed outlier: 4.009A pdb=" N MET C3239 " --> pdb=" O SER C3235 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N CYS C3240 " --> pdb=" O VAL C3236 " (cutoff:3.500A) Proline residue: C3241 - end of helix No H-bonds generated for 'chain 'C' and resid 3235 through 3241' Processing helix chain 'C' and resid 3245 through 3260 removed outlier: 3.859A pdb=" N SER C3259 " --> pdb=" O GLY C3255 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY C3260 " --> pdb=" O LEU C3256 " (cutoff:3.500A) Processing helix chain 'C' and resid 3262 through 3267 Proline residue: C3267 - end of helix Processing helix chain 'C' and resid 3268 through 3288 removed outlier: 4.245A pdb=" N LEU C3274 " --> pdb=" O ILE C3270 " (cutoff:3.500A) Proline residue: C3275 - end of helix Proline residue: C3282 - end of helix removed outlier: 4.085A pdb=" N GLU C3286 " --> pdb=" O PRO C3282 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG C3287 " --> pdb=" O ARG C3283 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY C3288 " --> pdb=" O TRP C3284 " (cutoff:3.500A) Processing helix chain 'C' and resid 3308 through 3327 removed outlier: 3.623A pdb=" N LEU C3312 " --> pdb=" O THR C3308 " (cutoff:3.500A) Processing helix chain 'C' and resid 3333 through 3347 removed outlier: 4.171A pdb=" N ARG C3337 " --> pdb=" O THR C3333 " (cutoff:3.500A) Proline residue: C3344 - end of helix removed outlier: 4.406A pdb=" N SER C3347 " --> pdb=" O GLN C3343 " (cutoff:3.500A) Processing helix chain 'C' and resid 3350 through 3383 removed outlier: 4.024A pdb=" N LEU C3354 " --> pdb=" O ARG C3350 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS C3355 " --> pdb=" O PRO C3351 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE C3359 " --> pdb=" O HIS C3355 " (cutoff:3.500A) Proline residue: C3360 - end of helix removed outlier: 3.872A pdb=" N GLU C3382 " --> pdb=" O GLN C3378 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA C3383 " --> pdb=" O LEU C3379 " (cutoff:3.500A) Processing helix chain 'C' and resid 3384 through 3420 removed outlier: 4.307A pdb=" N GLU C3388 " --> pdb=" O LYS C3384 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY C3390 " --> pdb=" O GLU C3386 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C3392 " --> pdb=" O GLU C3388 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C3393 " --> pdb=" O GLU C3389 " (cutoff:3.500A) Proline residue: C3410 - end of helix removed outlier: 3.575A pdb=" N ASN C3418 " --> pdb=" O ARG C3414 " (cutoff:3.500A) Processing helix chain 'C' and resid 3421 through 3427 Proline residue: C3427 - end of helix Processing helix chain 'C' and resid 3428 through 3449 removed outlier: 4.818A pdb=" N HIS C3449 " --> pdb=" O TRP C3445 " (cutoff:3.500A) Processing helix chain 'C' and resid 3450 through 3463 removed outlier: 3.607A pdb=" N GLN C3461 " --> pdb=" O ASN C3457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C3462 " --> pdb=" O PHE C3458 " (cutoff:3.500A) Processing helix chain 'C' and resid 3465 through 3478 removed outlier: 6.759A pdb=" N PHE C3469 " --> pdb=" O ASN C3465 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C3470 " --> pdb=" O ASN C3466 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASP C3473 " --> pdb=" O PHE C3469 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER C3474 " --> pdb=" O LEU C3470 " (cutoff:3.500A) Processing helix chain 'C' and resid 3508 through 3526 removed outlier: 3.567A pdb=" N LEU C3514 " --> pdb=" O ILE C3510 " (cutoff:3.500A) Proline residue: C3519 - end of helix removed outlier: 3.705A pdb=" N MET C3524 " --> pdb=" O ILE C3520 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS C3525 " --> pdb=" O GLY C3521 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALA C3526 " --> pdb=" O LEU C3522 " (cutoff:3.500A) Processing helix chain 'C' and resid 3527 through 3543 removed outlier: 5.221A pdb=" N ASP C3531 " --> pdb=" O PRO C3527 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU C3532 " --> pdb=" O THR C3528 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C3537 " --> pdb=" O ILE C3533 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C3538 " --> pdb=" O MET C3534 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C3543 " --> pdb=" O ARG C3539 " (cutoff:3.500A) Processing helix chain 'C' and resid 3545 through 3557 Processing helix chain 'C' and resid 3562 through 3567 removed outlier: 3.673A pdb=" N SER C3566 " --> pdb=" O LYS C3562 " (cutoff:3.500A) Proline residue: C3567 - end of helix No H-bonds generated for 'chain 'C' and resid 3562 through 3567' Processing helix chain 'C' and resid 3568 through 3580 removed outlier: 3.734A pdb=" N GLN C3572 " --> pdb=" O SER C3568 " (cutoff:3.500A) Proline residue: C3580 - end of helix Processing helix chain 'C' and resid 3588 through 3612 removed outlier: 3.702A pdb=" N ARG C3594 " --> pdb=" O GLU C3590 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C3607 " --> pdb=" O LEU C3603 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C3608 " --> pdb=" O TYR C3604 " (cutoff:3.500A) Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3628 through 3638 removed outlier: 3.876A pdb=" N VAL C3632 " --> pdb=" O ARG C3628 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE C3636 " --> pdb=" O VAL C3632 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG C3637 " --> pdb=" O VAL C3633 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3665 removed outlier: 3.690A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU C3663 " --> pdb=" O ALA C3659 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N THR C3664 " --> pdb=" O ALA C3660 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3679 removed outlier: 3.757A pdb=" N LYS C3679 " --> pdb=" O ASP C3675 " (cutoff:3.500A) Processing helix chain 'C' and resid 3696 through 3711 removed outlier: 3.547A pdb=" N VAL C3702 " --> pdb=" O LEU C3698 " (cutoff:3.500A) Processing helix chain 'C' and resid 3719 through 3735 removed outlier: 4.128A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N HIS C3734 " --> pdb=" O ALA C3730 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU C3735 " --> pdb=" O LYS C3731 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3772 removed outlier: 4.679A pdb=" N MET C3758 " --> pdb=" O GLU C3754 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C3759 " --> pdb=" O GLU C3755 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C3760 " --> pdb=" O LYS C3756 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C3770 " --> pdb=" O GLN C3766 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 4.485A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3826 through 3839 Processing helix chain 'C' and resid 3843 through 3857 Processing helix chain 'C' and resid 3877 through 3893 Processing helix chain 'C' and resid 3896 through 3905 Processing helix chain 'C' and resid 3914 through 3939 removed outlier: 3.766A pdb=" N TYR C3937 " --> pdb=" O PHE C3933 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C3939 " --> pdb=" O TRP C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3970 Processing helix chain 'C' and resid 3973 through 3983 Processing helix chain 'C' and resid 3984 through 4007 removed outlier: 3.799A pdb=" N ALA C3988 " --> pdb=" O ARG C3984 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP C4006 " --> pdb=" O LYS C4002 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER C4007 " --> pdb=" O LEU C4003 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.729A pdb=" N LEU C4019 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C4020 " --> pdb=" O LEU C4016 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C4032 " --> pdb=" O LEU C4028 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4052 Processing helix chain 'C' and resid 4053 through 4072 removed outlier: 3.793A pdb=" N MET C4064 " --> pdb=" O LYS C4060 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS C4069 " --> pdb=" O PHE C4065 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4082 removed outlier: 5.008A pdb=" N THR C4082 " --> pdb=" O GLN C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4101 removed outlier: 3.579A pdb=" N MET C4097 " --> pdb=" O PHE C4093 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP C4098 " --> pdb=" O GLN C4094 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER C4099 " --> pdb=" O LYS C4095 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN C4100 " --> pdb=" O ALA C4096 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C4101 " --> pdb=" O MET C4097 " (cutoff:3.500A) Processing helix chain 'C' and resid 4104 through 4116 removed outlier: 5.475A pdb=" N GLU C4116 " --> pdb=" O LEU C4112 " (cutoff:3.500A) Processing helix chain 'C' and resid 4124 through 4134 removed outlier: 3.642A pdb=" N PHE C4128 " --> pdb=" O ASN C4124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C4129 " --> pdb=" O PHE C4125 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN C4130 " --> pdb=" O GLU C4126 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE C4132 " --> pdb=" O PHE C4128 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLN C4133 " --> pdb=" O ALA C4129 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU C4134 " --> pdb=" O ASN C4130 " (cutoff:3.500A) Processing helix chain 'C' and resid 4135 through 4155 removed outlier: 3.892A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) Proline residue: C4155 - end of helix Processing helix chain 'C' and resid 4157 through 4168 removed outlier: 3.738A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN C4162 " --> pdb=" O PRO C4158 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C4163 " --> pdb=" O ARG C4159 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C4164 " --> pdb=" O LEU C4160 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C4165 " --> pdb=" O ARG C4161 " (cutoff:3.500A) Processing helix chain 'C' and resid 4169 through 4176 removed outlier: 3.663A pdb=" N TYR C4173 " --> pdb=" O SER C4169 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C4174 " --> pdb=" O ILE C4170 " (cutoff:3.500A) Proline residue: C4176 - end of helix Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4208 through 4224 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4540 through 4559 Processing helix chain 'C' and resid 4560 through 4580 removed outlier: 3.752A pdb=" N LEU C4578 " --> pdb=" O ASN C4574 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR C4580 " --> pdb=" O ILE C4576 " (cutoff:3.500A) Processing helix chain 'C' and resid 4640 through 4683 removed outlier: 3.599A pdb=" N ILE C4658 " --> pdb=" O ALA C4654 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C4666 " --> pdb=" O ASN C4662 " (cutoff:3.500A) Proline residue: C4667 - end of helix Processing helix chain 'C' and resid 4696 through 4709 removed outlier: 4.394A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR C4708 " --> pdb=" O LEU C4704 " (cutoff:3.500A) Proline residue: C4709 - end of helix Processing helix chain 'C' and resid 4719 through 4729 Processing helix chain 'C' and resid 4733 through 4742 removed outlier: 4.143A pdb=" N ILE C4737 " --> pdb=" O GLY C4733 " (cutoff:3.500A) Processing helix chain 'C' and resid 4744 through 4750 removed outlier: 4.107A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE C4750 " --> pdb=" O ALA C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4772 through 4786 Processing helix chain 'C' and resid 4787 through 4805 removed outlier: 4.044A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4808 through 4820 removed outlier: 5.031A pdb=" N HIS C4812 " --> pdb=" O PHE C4808 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU C4813 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU C4814 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASP C4815 " --> pdb=" O ALA C4811 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE C4816 " --> pdb=" O HIS C4812 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA C4817 " --> pdb=" O LEU C4813 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.871A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4858 Processing helix chain 'C' and resid 4859 through 4864 removed outlier: 4.272A pdb=" N TYR C4863 " --> pdb=" O PHE C4859 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN C4864 " --> pdb=" O ARG C4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4859 through 4864' Processing helix chain 'C' and resid 4878 through 4893 removed outlier: 4.368A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4896 through 4901 removed outlier: 4.471A pdb=" N GLU C4900 " --> pdb=" O GLY C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4924 Processing helix chain 'C' and resid 4928 through 4957 removed outlier: 4.505A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4964 through 4970 removed outlier: 3.997A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 4999 through 5004 removed outlier: 3.817A pdb=" N HIS C5003 " --> pdb=" O ASP C4999 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THR C5004 " --> pdb=" O GLU C5000 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4999 through 5004' Processing helix chain 'C' and resid 5005 through 5017 Processing helix chain 'C' and resid 5027 through 5033 Processing helix chain 'D' and resid 61 through 66 removed outlier: 4.221A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 66' Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.519A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 255' Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.928A pdb=" N ALA D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 364 through 370 removed outlier: 3.756A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 423 removed outlier: 3.695A pdb=" N HIS D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY D 423 " --> pdb=" O ASP D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 453 Processing helix chain 'D' and resid 461 through 482 removed outlier: 3.762A pdb=" N GLN D 465 " --> pdb=" O HIS D 461 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 3.518A pdb=" N LEU D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.085A pdb=" N TYR D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 531 removed outlier: 4.519A pdb=" N LYS D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 544 removed outlier: 3.862A pdb=" N PHE D 540 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 551 removed outlier: 3.758A pdb=" N LYS D 550 " --> pdb=" O TRP D 546 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 4.239A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 567 " --> pdb=" O VAL D 563 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU D 570 " --> pdb=" O CYS D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 579 removed outlier: 3.998A pdb=" N ASN D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 577 " --> pdb=" O GLU D 573 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 572 through 579' Processing helix chain 'D' and resid 580 through 593 removed outlier: 3.774A pdb=" N LEU D 590 " --> pdb=" O ILE D 586 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 609 removed outlier: 4.053A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N CYS D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 629 removed outlier: 4.242A pdb=" N LEU D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 626 " --> pdb=" O THR D 622 " (cutoff:3.500A) Proline residue: D 627 - end of helix Processing helix chain 'D' and resid 810 through 815 removed outlier: 4.680A pdb=" N ALA D 814 " --> pdb=" O PRO D 810 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 815 " --> pdb=" O CYS D 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 810 through 815' Processing helix chain 'D' and resid 847 through 853 removed outlier: 3.953A pdb=" N PHE D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL D 852 " --> pdb=" O HIS D 848 " (cutoff:3.500A) Proline residue: D 853 - end of helix No H-bonds generated for 'chain 'D' and resid 847 through 853' Processing helix chain 'D' and resid 864 through 885 removed outlier: 3.533A pdb=" N ILE D 870 " --> pdb=" O HIS D 866 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU D 872 " --> pdb=" O GLU D 868 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS D 873 " --> pdb=" O ARG D 869 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 875 " --> pdb=" O ARG D 871 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU D 880 " --> pdb=" O GLU D 876 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU D 881 " --> pdb=" O ASN D 877 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TRP D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA D 883 " --> pdb=" O HIS D 879 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 914 removed outlier: 3.812A pdb=" N LEU D 913 " --> pdb=" O ASN D 909 " (cutoff:3.500A) Proline residue: D 914 - end of helix No H-bonds generated for 'chain 'D' and resid 909 through 914' Processing helix chain 'D' and resid 915 through 936 Processing helix chain 'D' and resid 945 through 950 removed outlier: 3.919A pdb=" N ASN D 949 " --> pdb=" O LYS D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 1004 removed outlier: 3.524A pdb=" N VAL D 995 " --> pdb=" O ASN D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1048 removed outlier: 4.041A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1072 removed outlier: 4.635A pdb=" N ARG D1071 " --> pdb=" O SER D1067 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL D1072 " --> pdb=" O ARG D1068 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1067 through 1072' Processing helix chain 'D' and resid 1207 through 1212 removed outlier: 3.941A pdb=" N LEU D1211 " --> pdb=" O ASP D1207 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG D1212 " --> pdb=" O VAL D1208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1207 through 1212' Processing helix chain 'D' and resid 1213 through 1218 removed outlier: 3.728A pdb=" N GLY D1218 " --> pdb=" O PHE D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1430 removed outlier: 3.584A pdb=" N LEU D1428 " --> pdb=" O PRO D1424 " (cutoff:3.500A) Processing helix chain 'D' and resid 1444 through 1449 removed outlier: 3.932A pdb=" N VAL D1448 " --> pdb=" O GLU D1444 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TRP D1449 " --> pdb=" O PRO D1445 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1444 through 1449' Processing helix chain 'D' and resid 1496 through 1501 removed outlier: 4.589A pdb=" N PHE D1500 " --> pdb=" O TRP D1496 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D1501 " --> pdb=" O GLY D1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1496 through 1501' Processing helix chain 'D' and resid 1574 through 1581 removed outlier: 3.802A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE D1580 " --> pdb=" O SER D1576 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU D1581 " --> pdb=" O ALA D1577 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1657 removed outlier: 4.260A pdb=" N LEU D1653 " --> pdb=" O ASP D1649 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER D1654 " --> pdb=" O ILE D1650 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU D1655 " --> pdb=" O LEU D1651 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU D1657 " --> pdb=" O LEU D1653 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.758A pdb=" N PHE D1662 " --> pdb=" O ASP D1658 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS D1674 " --> pdb=" O TYR D1670 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1689 removed outlier: 3.530A pdb=" N CYS D1686 " --> pdb=" O ALA D1682 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1690 through 1700 removed outlier: 3.625A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1719 Processing helix chain 'D' and resid 1720 through 1734 removed outlier: 3.992A pdb=" N SER D1732 " --> pdb=" O ARG D1728 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU D1733 " --> pdb=" O SER D1729 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR D1734 " --> pdb=" O MET D1730 " (cutoff:3.500A) Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.836A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1825 removed outlier: 3.641A pdb=" N HIS D1825 " --> pdb=" O ASP D1821 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1867 Processing helix chain 'D' and resid 1925 through 1930 removed outlier: 4.323A pdb=" N MET D1929 " --> pdb=" O GLY D1925 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS D1930 " --> pdb=" O LEU D1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1925 through 1930' Processing helix chain 'D' and resid 1934 through 1987 removed outlier: 3.828A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D1945 " --> pdb=" O ASN D1941 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP D1967 " --> pdb=" O GLU D1963 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D1982 " --> pdb=" O ALA D1978 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE D1984 " --> pdb=" O LEU D1980 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR D1985 " --> pdb=" O MET D1981 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET D1986 " --> pdb=" O ARG D1982 " (cutoff:3.500A) Processing helix chain 'D' and resid 1990 through 2000 removed outlier: 4.256A pdb=" N ARG D1994 " --> pdb=" O GLU D1990 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU D1997 " --> pdb=" O ARG D1993 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N PHE D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2001 through 2011 removed outlier: 3.696A pdb=" N ASN D2007 " --> pdb=" O GLN D2003 " (cutoff:3.500A) Processing helix chain 'D' and resid 2017 through 2022 removed outlier: 3.540A pdb=" N CYS D2021 " --> pdb=" O ASP D2017 " (cutoff:3.500A) Proline residue: D2022 - end of helix No H-bonds generated for 'chain 'D' and resid 2017 through 2022' Processing helix chain 'D' and resid 2024 through 2043 Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.611A pdb=" N SER D2099 " --> pdb=" O GLN D2095 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 4.115A pdb=" N GLY D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2142 Proline residue: D2139 - end of helix removed outlier: 5.390A pdb=" N TYR D2142 " --> pdb=" O LEU D2138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2145 through 2169 removed outlier: 3.714A pdb=" N VAL D2149 " --> pdb=" O SER D2145 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU D2150 " --> pdb=" O PRO D2146 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASP D2151 " --> pdb=" O SER D2147 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN D2161 " --> pdb=" O GLU D2157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D2162 " --> pdb=" O CYS D2158 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D2166 " --> pdb=" O ILE D2162 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE D2167 " --> pdb=" O ARG D2163 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL D2168 " --> pdb=" O SER D2164 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN D2169 " --> pdb=" O LEU D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2171 through 2189 removed outlier: 5.449A pdb=" N LYS D2189 " --> pdb=" O ILE D2185 " (cutoff:3.500A) Processing helix chain 'D' and resid 2190 through 2195 Proline residue: D2195 - end of helix Processing helix chain 'D' and resid 2196 through 2219 removed outlier: 3.639A pdb=" N GLY D2202 " --> pdb=" O MET D2198 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N MET D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N HIS D2204 " --> pdb=" O ALA D2200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU D2205 " --> pdb=" O LEU D2201 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D2214 " --> pdb=" O VAL D2210 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY D2218 " --> pdb=" O VAL D2214 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D2219 " --> pdb=" O LEU D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2225 through 2244 removed outlier: 3.915A pdb=" N VAL D2229 " --> pdb=" O PHE D2225 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D2241 " --> pdb=" O CYS D2237 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG D2244 " --> pdb=" O CYS D2240 " (cutoff:3.500A) Processing helix chain 'D' and resid 2245 through 2254 removed outlier: 4.346A pdb=" N HIS D2253 " --> pdb=" O SER D2249 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D2254 " --> pdb=" O MET D2250 " (cutoff:3.500A) Processing helix chain 'D' and resid 2255 through 2265 removed outlier: 3.916A pdb=" N GLY D2262 " --> pdb=" O LEU D2258 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE D2263 " --> pdb=" O GLU D2259 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY D2264 " --> pdb=" O ASN D2260 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU D2265 " --> pdb=" O SER D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2281 removed outlier: 3.687A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2291 through 2308 Processing helix chain 'D' and resid 2310 through 2317 removed outlier: 3.727A pdb=" N GLY D2317 " --> pdb=" O LEU D2313 " (cutoff:3.500A) Processing helix chain 'D' and resid 2324 through 2340 removed outlier: 3.656A pdb=" N PHE D2334 " --> pdb=" O ARG D2330 " (cutoff:3.500A) Processing helix chain 'D' and resid 2346 through 2361 removed outlier: 3.567A pdb=" N ASN D2351 " --> pdb=" O GLU D2347 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Proline residue: D2361 - end of helix Processing helix chain 'D' and resid 2375 through 2390 Proline residue: D2390 - end of helix Processing helix chain 'D' and resid 2417 through 2437 Processing helix chain 'D' and resid 2439 through 2446 removed outlier: 3.854A pdb=" N ALA D2445 " --> pdb=" O HIS D2441 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D2446 " --> pdb=" O LEU D2442 " (cutoff:3.500A) Processing helix chain 'D' and resid 2447 through 2462 Proline residue: D2462 - end of helix Processing helix chain 'D' and resid 2463 through 2472 Processing helix chain 'D' and resid 2495 through 2509 removed outlier: 3.972A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D2505 " --> pdb=" O SER D2501 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2525 removed outlier: 3.737A pdb=" N VAL D2524 " --> pdb=" O HIS D2520 " (cutoff:3.500A) Processing helix chain 'D' and resid 2526 through 2538 removed outlier: 5.112A pdb=" N THR D2538 " --> pdb=" O ALA D2534 " (cutoff:3.500A) Processing helix chain 'D' and resid 2540 through 2545 removed outlier: 4.593A pdb=" N THR D2544 " --> pdb=" O THR D2540 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU D2545 " --> pdb=" O PHE D2541 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2540 through 2545' Processing helix chain 'D' and resid 2546 through 2566 removed outlier: 5.515A pdb=" N LEU D2559 " --> pdb=" O CYS D2555 " (cutoff:3.500A) Proline residue: D2560 - end of helix Processing helix chain 'D' and resid 2575 through 2592 removed outlier: 3.700A pdb=" N VAL D2579 " --> pdb=" O ARG D2575 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D2592 " --> pdb=" O ARG D2588 " (cutoff:3.500A) Processing helix chain 'D' and resid 2596 through 2614 removed outlier: 4.088A pdb=" N VAL D2602 " --> pdb=" O ALA D2598 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D2603 " --> pdb=" O GLN D2599 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D2604 " --> pdb=" O ARG D2600 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR D2613 " --> pdb=" O ALA D2609 " (cutoff:3.500A) Processing helix chain 'D' and resid 2615 through 2630 removed outlier: 3.846A pdb=" N LEU D2619 " --> pdb=" O ARG D2615 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D2620 " --> pdb=" O PRO D2616 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS D2621 " --> pdb=" O SER D2617 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU D2622 " --> pdb=" O MET D2618 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE D2628 " --> pdb=" O ARG D2624 " (cutoff:3.500A) Processing helix chain 'D' and resid 2637 through 2652 removed outlier: 3.543A pdb=" N LEU D2641 " --> pdb=" O ALA D2637 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D2642 " --> pdb=" O LYS D2638 " (cutoff:3.500A) Processing helix chain 'D' and resid 2668 through 2690 removed outlier: 6.747A pdb=" N LEU D2672 " --> pdb=" O SER D2668 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS D2673 " --> pdb=" O GLU D2669 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYS D2690 " --> pdb=" O LEU D2686 " (cutoff:3.500A) Processing helix chain 'D' and resid 2693 through 2711 removed outlier: 3.888A pdb=" N MET D2698 " --> pdb=" O GLU D2694 " (cutoff:3.500A) Proline residue: D2701 - end of helix Proline residue: D2711 - end of helix Processing helix chain 'D' and resid 2748 through 2774 removed outlier: 4.978A pdb=" N ASP D2752 " --> pdb=" O PRO D2748 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER D2753 " --> pdb=" O GLU D2749 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE D2754 " --> pdb=" O LYS D2750 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D2757 " --> pdb=" O SER D2753 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN D2774 " --> pdb=" O LYS D2770 " (cutoff:3.500A) Processing helix chain 'D' and resid 2798 through 2820 removed outlier: 4.314A pdb=" N LYS D2802 " --> pdb=" O SER D2798 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG D2806 " --> pdb=" O LYS D2802 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TRP D2807 " --> pdb=" O GLU D2803 " (cutoff:3.500A) Proline residue: D2808 - end of helix removed outlier: 3.747A pdb=" N ALA D2818 " --> pdb=" O LYS D2814 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TRP D2819 " --> pdb=" O ALA D2815 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU D2820 " --> pdb=" O MET D2816 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2895 removed outlier: 4.626A pdb=" N GLU D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2934 removed outlier: 4.984A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D2922 " --> pdb=" O ARG D2918 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D2933 " --> pdb=" O PHE D2929 " (cutoff:3.500A) Processing helix chain 'D' and resid 2949 through 2954 removed outlier: 3.781A pdb=" N ARG D2954 " --> pdb=" O SER D2950 " (cutoff:3.500A) Processing helix chain 'D' and resid 2955 through 2982 removed outlier: 4.332A pdb=" N ILE D2969 " --> pdb=" O ARG D2965 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA D2975 " --> pdb=" O GLN D2971 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS D2976 " --> pdb=" O GLU D2972 " (cutoff:3.500A) Processing helix chain 'D' and resid 2991 through 3014 removed outlier: 4.866A pdb=" N LEU D3003 " --> pdb=" O ALA D2999 " (cutoff:3.500A) Proline residue: D3004 - end of helix Processing helix chain 'D' and resid 3032 through 3051 removed outlier: 3.898A pdb=" N THR D3040 " --> pdb=" O LYS D3036 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER D3041 " --> pdb=" O GLU D3037 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D3047 " --> pdb=" O PHE D3043 " (cutoff:3.500A) Processing helix chain 'D' and resid 3053 through 3058 removed outlier: 3.862A pdb=" N PHE D3057 " --> pdb=" O ARG D3053 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY D3058 " --> pdb=" O VAL D3054 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3053 through 3058' Processing helix chain 'D' and resid 3060 through 3075 Processing helix chain 'D' and resid 3076 through 3083 Processing helix chain 'D' and resid 3085 through 3112 removed outlier: 4.335A pdb=" N LEU D3112 " --> pdb=" O GLU D3108 " (cutoff:3.500A) Processing helix chain 'D' and resid 3123 through 3151 removed outlier: 3.607A pdb=" N THR D3133 " --> pdb=" O LEU D3129 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU D3137 " --> pdb=" O THR D3133 " (cutoff:3.500A) Proline residue: D3138 - end of helix removed outlier: 3.540A pdb=" N HIS D3150 " --> pdb=" O HIS D3146 " (cutoff:3.500A) Processing helix chain 'D' and resid 3159 through 3176 removed outlier: 4.854A pdb=" N VAL D3163 " --> pdb=" O ASP D3159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D3175 " --> pdb=" O SER D3171 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY D3176 " --> pdb=" O ILE D3172 " (cutoff:3.500A) Processing helix chain 'D' and resid 3180 through 3201 Proline residue: D3188 - end of helix removed outlier: 3.534A pdb=" N ARG D3196 " --> pdb=" O GLU D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3207 through 3212 removed outlier: 4.630A pdb=" N GLU D3212 " --> pdb=" O PRO D3208 " (cutoff:3.500A) Processing helix chain 'D' and resid 3217 through 3222 Processing helix chain 'D' and resid 3223 through 3231 removed outlier: 4.772A pdb=" N ARG D3227 " --> pdb=" O SER D3223 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA D3228 " --> pdb=" O PRO D3224 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE D3229 " --> pdb=" O ARG D3225 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU D3230 " --> pdb=" O GLU D3226 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3223 through 3231' Processing helix chain 'D' and resid 3235 through 3241 removed outlier: 4.007A pdb=" N MET D3239 " --> pdb=" O SER D3235 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N CYS D3240 " --> pdb=" O VAL D3236 " (cutoff:3.500A) Proline residue: D3241 - end of helix No H-bonds generated for 'chain 'D' and resid 3235 through 3241' Processing helix chain 'D' and resid 3245 through 3260 removed outlier: 3.859A pdb=" N SER D3259 " --> pdb=" O GLY D3255 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY D3260 " --> pdb=" O LEU D3256 " (cutoff:3.500A) Processing helix chain 'D' and resid 3262 through 3267 Proline residue: D3267 - end of helix Processing helix chain 'D' and resid 3268 through 3288 removed outlier: 4.244A pdb=" N LEU D3274 " --> pdb=" O ILE D3270 " (cutoff:3.500A) Proline residue: D3275 - end of helix Proline residue: D3282 - end of helix removed outlier: 4.084A pdb=" N GLU D3286 " --> pdb=" O PRO D3282 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG D3287 " --> pdb=" O ARG D3283 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY D3288 " --> pdb=" O TRP D3284 " (cutoff:3.500A) Processing helix chain 'D' and resid 3308 through 3327 removed outlier: 3.622A pdb=" N LEU D3312 " --> pdb=" O THR D3308 " (cutoff:3.500A) Processing helix chain 'D' and resid 3333 through 3347 removed outlier: 4.171A pdb=" N ARG D3337 " --> pdb=" O THR D3333 " (cutoff:3.500A) Proline residue: D3344 - end of helix removed outlier: 4.406A pdb=" N SER D3347 " --> pdb=" O GLN D3343 " (cutoff:3.500A) Processing helix chain 'D' and resid 3350 through 3383 removed outlier: 4.025A pdb=" N LEU D3354 " --> pdb=" O ARG D3350 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS D3355 " --> pdb=" O PRO D3351 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE D3359 " --> pdb=" O HIS D3355 " (cutoff:3.500A) Proline residue: D3360 - end of helix removed outlier: 3.874A pdb=" N GLU D3382 " --> pdb=" O GLN D3378 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA D3383 " --> pdb=" O LEU D3379 " (cutoff:3.500A) Processing helix chain 'D' and resid 3384 through 3420 removed outlier: 4.307A pdb=" N GLU D3388 " --> pdb=" O LYS D3384 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY D3390 " --> pdb=" O GLU D3386 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D3392 " --> pdb=" O GLU D3388 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU D3393 " --> pdb=" O GLU D3389 " (cutoff:3.500A) Proline residue: D3410 - end of helix removed outlier: 3.575A pdb=" N ASN D3418 " --> pdb=" O ARG D3414 " (cutoff:3.500A) Processing helix chain 'D' and resid 3421 through 3427 Proline residue: D3427 - end of helix Processing helix chain 'D' and resid 3428 through 3449 removed outlier: 4.819A pdb=" N HIS D3449 " --> pdb=" O TRP D3445 " (cutoff:3.500A) Processing helix chain 'D' and resid 3450 through 3463 removed outlier: 3.607A pdb=" N GLN D3461 " --> pdb=" O ASN D3457 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN D3462 " --> pdb=" O PHE D3458 " (cutoff:3.500A) Processing helix chain 'D' and resid 3465 through 3478 removed outlier: 6.759A pdb=" N PHE D3469 " --> pdb=" O ASN D3465 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU D3470 " --> pdb=" O ASN D3466 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP D3473 " --> pdb=" O PHE D3469 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER D3474 " --> pdb=" O LEU D3470 " (cutoff:3.500A) Processing helix chain 'D' and resid 3508 through 3526 removed outlier: 3.567A pdb=" N LEU D3514 " --> pdb=" O ILE D3510 " (cutoff:3.500A) Proline residue: D3519 - end of helix removed outlier: 3.706A pdb=" N MET D3524 " --> pdb=" O ILE D3520 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS D3525 " --> pdb=" O GLY D3521 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA D3526 " --> pdb=" O LEU D3522 " (cutoff:3.500A) Processing helix chain 'D' and resid 3527 through 3543 removed outlier: 5.221A pdb=" N ASP D3531 " --> pdb=" O PRO D3527 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU D3532 " --> pdb=" O THR D3528 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D3537 " --> pdb=" O ILE D3533 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR D3538 " --> pdb=" O MET D3534 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D3543 " --> pdb=" O ARG D3539 " (cutoff:3.500A) Processing helix chain 'D' and resid 3545 through 3557 Processing helix chain 'D' and resid 3562 through 3567 removed outlier: 3.673A pdb=" N SER D3566 " --> pdb=" O LYS D3562 " (cutoff:3.500A) Proline residue: D3567 - end of helix No H-bonds generated for 'chain 'D' and resid 3562 through 3567' Processing helix chain 'D' and resid 3568 through 3580 removed outlier: 3.734A pdb=" N GLN D3572 " --> pdb=" O SER D3568 " (cutoff:3.500A) Proline residue: D3580 - end of helix Processing helix chain 'D' and resid 3588 through 3612 removed outlier: 3.702A pdb=" N ARG D3594 " --> pdb=" O GLU D3590 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D3607 " --> pdb=" O LEU D3603 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN D3608 " --> pdb=" O TYR D3604 " (cutoff:3.500A) Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3628 through 3638 removed outlier: 3.876A pdb=" N VAL D3632 " --> pdb=" O ARG D3628 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE D3636 " --> pdb=" O VAL D3632 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG D3637 " --> pdb=" O VAL D3633 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3665 removed outlier: 3.690A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU D3663 " --> pdb=" O ALA D3659 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR D3664 " --> pdb=" O ALA D3660 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3679 removed outlier: 3.758A pdb=" N LYS D3679 " --> pdb=" O ASP D3675 " (cutoff:3.500A) Processing helix chain 'D' and resid 3696 through 3711 removed outlier: 3.546A pdb=" N VAL D3702 " --> pdb=" O LEU D3698 " (cutoff:3.500A) Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 4.128A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N HIS D3734 " --> pdb=" O ALA D3730 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU D3735 " --> pdb=" O LYS D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3772 removed outlier: 4.678A pdb=" N MET D3758 " --> pdb=" O GLU D3754 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU D3759 " --> pdb=" O GLU D3755 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D3760 " --> pdb=" O LYS D3756 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D3770 " --> pdb=" O GLN D3766 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.486A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3826 through 3839 Processing helix chain 'D' and resid 3843 through 3857 Processing helix chain 'D' and resid 3877 through 3893 Processing helix chain 'D' and resid 3896 through 3905 Processing helix chain 'D' and resid 3914 through 3939 removed outlier: 3.766A pdb=" N TYR D3937 " --> pdb=" O PHE D3933 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY D3939 " --> pdb=" O TRP D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3970 Processing helix chain 'D' and resid 3973 through 3983 Processing helix chain 'D' and resid 3984 through 4007 removed outlier: 3.799A pdb=" N ALA D3988 " --> pdb=" O ARG D3984 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP D4006 " --> pdb=" O LYS D4002 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N SER D4007 " --> pdb=" O LEU D4003 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.730A pdb=" N LEU D4019 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D4020 " --> pdb=" O LEU D4016 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D4032 " --> pdb=" O LEU D4028 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4052 Processing helix chain 'D' and resid 4053 through 4072 removed outlier: 3.793A pdb=" N MET D4064 " --> pdb=" O LYS D4060 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS D4069 " --> pdb=" O PHE D4065 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4082 removed outlier: 5.008A pdb=" N THR D4082 " --> pdb=" O GLN D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4101 removed outlier: 3.579A pdb=" N MET D4097 " --> pdb=" O PHE D4093 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP D4098 " --> pdb=" O GLN D4094 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER D4099 " --> pdb=" O LYS D4095 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN D4100 " --> pdb=" O ALA D4096 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS D4101 " --> pdb=" O MET D4097 " (cutoff:3.500A) Processing helix chain 'D' and resid 4104 through 4116 removed outlier: 5.475A pdb=" N GLU D4116 " --> pdb=" O LEU D4112 " (cutoff:3.500A) Processing helix chain 'D' and resid 4124 through 4134 removed outlier: 3.642A pdb=" N PHE D4128 " --> pdb=" O ASN D4124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D4129 " --> pdb=" O PHE D4125 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN D4130 " --> pdb=" O GLU D4126 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE D4132 " --> pdb=" O PHE D4128 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLN D4133 " --> pdb=" O ALA D4129 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU D4134 " --> pdb=" O ASN D4130 " (cutoff:3.500A) Processing helix chain 'D' and resid 4135 through 4155 removed outlier: 3.892A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) Proline residue: D4155 - end of helix Processing helix chain 'D' and resid 4157 through 4168 removed outlier: 3.739A pdb=" N ARG D4161 " --> pdb=" O ASP D4157 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN D4162 " --> pdb=" O PRO D4158 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE D4163 " --> pdb=" O ARG D4159 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D4164 " --> pdb=" O LEU D4160 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D4165 " --> pdb=" O ARG D4161 " (cutoff:3.500A) Processing helix chain 'D' and resid 4169 through 4176 removed outlier: 3.663A pdb=" N TYR D4173 " --> pdb=" O SER D4169 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D4174 " --> pdb=" O ILE D4170 " (cutoff:3.500A) Proline residue: D4176 - end of helix Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4540 through 4559 Processing helix chain 'D' and resid 4560 through 4580 removed outlier: 3.752A pdb=" N LEU D4578 " --> pdb=" O ASN D4574 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR D4580 " --> pdb=" O ILE D4576 " (cutoff:3.500A) Processing helix chain 'D' and resid 4640 through 4683 removed outlier: 3.599A pdb=" N ILE D4658 " --> pdb=" O ALA D4654 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D4666 " --> pdb=" O ASN D4662 " (cutoff:3.500A) Proline residue: D4667 - end of helix Processing helix chain 'D' and resid 4696 through 4709 removed outlier: 4.395A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR D4708 " --> pdb=" O LEU D4704 " (cutoff:3.500A) Proline residue: D4709 - end of helix Processing helix chain 'D' and resid 4719 through 4729 Processing helix chain 'D' and resid 4733 through 4742 removed outlier: 4.143A pdb=" N ILE D4737 " --> pdb=" O GLY D4733 " (cutoff:3.500A) Processing helix chain 'D' and resid 4744 through 4750 removed outlier: 4.107A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE D4750 " --> pdb=" O ALA D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4772 through 4786 Processing helix chain 'D' and resid 4787 through 4805 removed outlier: 4.043A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4808 through 4820 removed outlier: 5.031A pdb=" N HIS D4812 " --> pdb=" O PHE D4808 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU D4813 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU D4814 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP D4815 " --> pdb=" O ALA D4811 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE D4816 " --> pdb=" O HIS D4812 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ALA D4817 " --> pdb=" O LEU D4813 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.871A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4858 Processing helix chain 'D' and resid 4859 through 4864 removed outlier: 4.273A pdb=" N TYR D4863 " --> pdb=" O PHE D4859 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASN D4864 " --> pdb=" O ARG D4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4859 through 4864' Processing helix chain 'D' and resid 4878 through 4893 removed outlier: 4.368A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4896 through 4901 removed outlier: 4.471A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4924 Processing helix chain 'D' and resid 4928 through 4957 removed outlier: 4.505A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 3.997A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 4999 through 5004 removed outlier: 3.818A pdb=" N HIS D5003 " --> pdb=" O ASP D4999 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N THR D5004 " --> pdb=" O GLU D5000 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4999 through 5004' Processing helix chain 'D' and resid 5005 through 5017 Processing helix chain 'D' and resid 5027 through 5033 Processing helix chain 'E' and resid 38 through 43 removed outlier: 5.186A pdb=" N ARG E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 67 removed outlier: 5.223A pdb=" N SER E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 43 removed outlier: 5.186A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 67 removed outlier: 5.223A pdb=" N SER F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 43 removed outlier: 5.186A pdb=" N ARG G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 67 removed outlier: 5.223A pdb=" N SER G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 5.186A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 67 removed outlier: 5.223A pdb=" N SER H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 49 through 52 removed outlier: 5.988A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 116 through 120 Processing sheet with id= 3, first strand: chain 'A' and resid 148 through 152 Processing sheet with id= 4, first strand: chain 'A' and resid 180 through 184 Processing sheet with id= 5, first strand: chain 'A' and resid 229 through 232 Processing sheet with id= 6, first strand: chain 'A' and resid 280 through 284 removed outlier: 4.059A pdb=" N HIS A 218 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A 221 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR A 391 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= 8, first strand: chain 'A' and resid 681 through 686 Processing sheet with id= 9, first strand: chain 'A' and resid 830 through 833 removed outlier: 4.387A pdb=" N LEU A1202 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN A1198 " --> pdb=" O GLY A 841 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A1199 " --> pdb=" O VAL A1095 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A1095 " --> pdb=" O VAL A1199 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 937 through 941 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'A' and resid 1129 through 1133 removed outlier: 4.003A pdb=" N GLY A1126 " --> pdb=" O MET A1100 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET A1100 " --> pdb=" O GLY A1126 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU A1099 " --> pdb=" O GLY A1195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A1194 " --> pdb=" O ARG A1073 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N THR A1235 " --> pdb=" O GLU A1078 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 1267 through 1272 removed outlier: 3.856A pdb=" N ILE A1562 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A1563 " --> pdb=" O ARG A1438 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY A1567 " --> pdb=" O TYR A1434 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR A1434 " --> pdb=" O GLY A1567 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR A1431 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY A1525 " --> pdb=" O VAL A1542 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 1485 through 1490 removed outlier: 3.917A pdb=" N GLY A1477 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLN A 765 " --> pdb=" O GLY A1477 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A 757 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 766 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE A 755 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N PHE A 768 " --> pdb=" O PRO A 753 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 754 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 742 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY A1625 " --> pdb=" O ALA A1620 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1550 through 1555 removed outlier: 5.982A pdb=" N PHE A1288 " --> pdb=" O LEU A1600 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A1600 " --> pdb=" O PHE A1288 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A1596 " --> pdb=" O SER A1292 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 4177 through 4184 removed outlier: 5.162A pdb=" N TYR A4177 " --> pdb=" O ILE A4197 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 4581 through 4584 removed outlier: 3.729A pdb=" N PHE A4631 " --> pdb=" O LYS A4581 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 49 through 52 removed outlier: 5.988A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 116 through 120 Processing sheet with id= 19, first strand: chain 'B' and resid 148 through 152 Processing sheet with id= 20, first strand: chain 'B' and resid 180 through 184 Processing sheet with id= 21, first strand: chain 'B' and resid 229 through 232 Processing sheet with id= 22, first strand: chain 'B' and resid 280 through 284 removed outlier: 4.059A pdb=" N HIS B 218 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 221 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 391 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 314 through 318 Processing sheet with id= 24, first strand: chain 'B' and resid 681 through 686 Processing sheet with id= 25, first strand: chain 'B' and resid 830 through 833 removed outlier: 4.388A pdb=" N LEU B1202 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN B1198 " --> pdb=" O GLY B 841 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL B1199 " --> pdb=" O VAL B1095 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B1095 " --> pdb=" O VAL B1199 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 937 through 941 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'B' and resid 1129 through 1133 removed outlier: 4.004A pdb=" N GLY B1126 " --> pdb=" O MET B1100 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET B1100 " --> pdb=" O GLY B1126 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU B1099 " --> pdb=" O GLY B1195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B1194 " --> pdb=" O ARG B1073 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR B1235 " --> pdb=" O GLU B1078 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'B' and resid 1267 through 1272 removed outlier: 3.856A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B1563 " --> pdb=" O ARG B1438 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY B1567 " --> pdb=" O TYR B1434 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR B1434 " --> pdb=" O GLY B1567 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR B1431 " --> pdb=" O LEU B1522 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY B1525 " --> pdb=" O VAL B1542 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 1485 through 1490 removed outlier: 3.917A pdb=" N GLY B1477 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLN B 765 " --> pdb=" O GLY B1477 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B 757 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY B 766 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE B 755 " --> pdb=" O GLY B 766 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE B 768 " --> pdb=" O PRO B 753 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY B1625 " --> pdb=" O ALA B1620 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 1550 through 1555 removed outlier: 5.981A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B1600 " --> pdb=" O PHE B1288 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B1596 " --> pdb=" O SER B1292 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 4177 through 4184 removed outlier: 5.162A pdb=" N TYR B4177 " --> pdb=" O ILE B4197 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 4581 through 4584 removed outlier: 3.728A pdb=" N PHE B4631 " --> pdb=" O LYS B4581 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 49 through 52 removed outlier: 5.987A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU C 19 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 116 through 120 Processing sheet with id= 35, first strand: chain 'C' and resid 148 through 152 Processing sheet with id= 36, first strand: chain 'C' and resid 180 through 184 Processing sheet with id= 37, first strand: chain 'C' and resid 229 through 232 Processing sheet with id= 38, first strand: chain 'C' and resid 280 through 284 removed outlier: 4.059A pdb=" N HIS C 218 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG C 221 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR C 391 " --> pdb=" O ARG C 221 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 314 through 318 Processing sheet with id= 40, first strand: chain 'C' and resid 681 through 686 Processing sheet with id= 41, first strand: chain 'C' and resid 830 through 833 removed outlier: 4.387A pdb=" N LEU C1202 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN C1198 " --> pdb=" O GLY C 841 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL C1199 " --> pdb=" O VAL C1095 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C1095 " --> pdb=" O VAL C1199 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 937 through 941 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'C' and resid 1129 through 1133 removed outlier: 4.003A pdb=" N GLY C1126 " --> pdb=" O MET C1100 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET C1100 " --> pdb=" O GLY C1126 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU C1099 " --> pdb=" O GLY C1195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C1194 " --> pdb=" O ARG C1073 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR C1235 " --> pdb=" O GLU C1078 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 1267 through 1272 removed outlier: 3.855A pdb=" N ILE C1562 " --> pdb=" O LEU C1272 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C1563 " --> pdb=" O ARG C1438 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY C1567 " --> pdb=" O TYR C1434 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N TYR C1434 " --> pdb=" O GLY C1567 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR C1431 " --> pdb=" O LEU C1522 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY C1525 " --> pdb=" O VAL C1542 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 1485 through 1490 removed outlier: 3.918A pdb=" N GLY C1477 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLN C 765 " --> pdb=" O GLY C1477 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE C 757 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C 766 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE C 755 " --> pdb=" O GLY C 766 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N PHE C 768 " --> pdb=" O PRO C 753 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C 754 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 742 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY C1625 " --> pdb=" O ALA C1620 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 1550 through 1555 removed outlier: 5.982A pdb=" N PHE C1288 " --> pdb=" O LEU C1600 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C1600 " --> pdb=" O PHE C1288 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU C1596 " --> pdb=" O SER C1292 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'C' and resid 4177 through 4184 removed outlier: 5.162A pdb=" N TYR C4177 " --> pdb=" O ILE C4197 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 4581 through 4584 removed outlier: 3.728A pdb=" N PHE C4631 " --> pdb=" O LYS C4581 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'D' and resid 49 through 52 removed outlier: 5.988A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU D 19 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'D' and resid 116 through 120 Processing sheet with id= 51, first strand: chain 'D' and resid 148 through 152 Processing sheet with id= 52, first strand: chain 'D' and resid 180 through 184 Processing sheet with id= 53, first strand: chain 'D' and resid 229 through 232 Processing sheet with id= 54, first strand: chain 'D' and resid 280 through 284 removed outlier: 4.058A pdb=" N HIS D 218 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG D 221 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR D 391 " --> pdb=" O ARG D 221 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'D' and resid 314 through 318 Processing sheet with id= 56, first strand: chain 'D' and resid 681 through 686 Processing sheet with id= 57, first strand: chain 'D' and resid 830 through 833 removed outlier: 4.388A pdb=" N LEU D1202 " --> pdb=" O PRO D 837 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN D1198 " --> pdb=" O GLY D 841 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL D1199 " --> pdb=" O VAL D1095 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D1095 " --> pdb=" O VAL D1199 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'D' and resid 937 through 941 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'D' and resid 1129 through 1133 removed outlier: 4.003A pdb=" N GLY D1126 " --> pdb=" O MET D1100 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET D1100 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU D1099 " --> pdb=" O GLY D1195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D1194 " --> pdb=" O ARG D1073 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR D1235 " --> pdb=" O GLU D1078 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'D' and resid 1267 through 1272 removed outlier: 3.856A pdb=" N ILE D1562 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D1563 " --> pdb=" O ARG D1438 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY D1567 " --> pdb=" O TYR D1434 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N TYR D1434 " --> pdb=" O GLY D1567 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N THR D1431 " --> pdb=" O LEU D1522 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLY D1525 " --> pdb=" O VAL D1542 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 1485 through 1490 removed outlier: 3.918A pdb=" N GLY D1477 " --> pdb=" O GLN D 765 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN D 765 " --> pdb=" O GLY D1477 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE D 757 " --> pdb=" O VAL D 764 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY D 766 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE D 755 " --> pdb=" O GLY D 766 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N PHE D 768 " --> pdb=" O PRO D 753 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP D 742 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY D1625 " --> pdb=" O ALA D1620 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 1550 through 1555 removed outlier: 5.981A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D1600 " --> pdb=" O PHE D1288 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU D1596 " --> pdb=" O SER D1292 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 4177 through 4184 removed outlier: 5.162A pdb=" N TYR D4177 " --> pdb=" O ILE D4197 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 4581 through 4584 removed outlier: 3.729A pdb=" N PHE D4631 " --> pdb=" O LYS D4581 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'E' and resid 2 through 7 removed outlier: 6.734A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 27 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 102 " --> pdb=" O HIS E 25 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.503A pdb=" N THR E 21 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'F' and resid 2 through 7 removed outlier: 6.734A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 27 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 102 " --> pdb=" O HIS F 25 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'F' and resid 21 through 24 removed outlier: 6.503A pdb=" N THR F 21 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'G' and resid 2 through 7 removed outlier: 6.734A pdb=" N ARG G 71 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR G 27 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 102 " --> pdb=" O HIS G 25 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'G' and resid 21 through 24 removed outlier: 6.503A pdb=" N THR G 21 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'H' and resid 2 through 7 removed outlier: 6.734A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR H 27 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU H 102 " --> pdb=" O HIS H 25 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'H' and resid 21 through 24 removed outlier: 6.503A pdb=" N THR H 21 " --> pdb=" O GLU H 107 " (cutoff:3.500A) 6900 hydrogen bonds defined for protein. 20600 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: 102.06 Time building geometry restraints manager: 46.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 36836 1.33 - 1.46: 37167 1.46 - 1.59: 70837 1.59 - 1.71: 12 1.71 - 1.84: 1512 Bond restraints: 146364 Sorted by residual: bond pdb=" C HIS C 904 " pdb=" N PRO C 905 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.45e+01 bond pdb=" C HIS B 904 " pdb=" N PRO B 905 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.45e+01 bond pdb=" C HIS A 904 " pdb=" N PRO A 905 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.45e+01 bond pdb=" C HIS D 904 " pdb=" N PRO D 905 " ideal model delta sigma weight residual 1.334 1.422 -0.089 2.34e-02 1.83e+03 1.43e+01 bond pdb=" CA PRO B1749 " pdb=" C PRO B1749 " ideal model delta sigma weight residual 1.514 1.498 0.016 5.50e-03 3.31e+04 8.88e+00 ... (remaining 146359 not shown) Histogram of bond angle deviations from ideal: 95.76 - 103.79: 2354 103.79 - 111.82: 64045 111.82 - 119.85: 64763 119.85 - 127.88: 65611 127.88 - 135.91: 1499 Bond angle restraints: 198272 Sorted by residual: angle pdb=" CA LYS B4581 " pdb=" CB LYS B4581 " pdb=" CG LYS B4581 " ideal model delta sigma weight residual 114.10 127.76 -13.66 2.00e+00 2.50e-01 4.67e+01 angle pdb=" CA LYS C4581 " pdb=" CB LYS C4581 " pdb=" CG LYS C4581 " ideal model delta sigma weight residual 114.10 127.75 -13.65 2.00e+00 2.50e-01 4.66e+01 angle pdb=" CA LYS A4581 " pdb=" CB LYS A4581 " pdb=" CG LYS A4581 " ideal model delta sigma weight residual 114.10 127.75 -13.65 2.00e+00 2.50e-01 4.66e+01 angle pdb=" CA LYS D4581 " pdb=" CB LYS D4581 " pdb=" CG LYS D4581 " ideal model delta sigma weight residual 114.10 127.72 -13.62 2.00e+00 2.50e-01 4.64e+01 angle pdb=" C MET D4184 " pdb=" N GLY D4185 " pdb=" CA GLY D4185 " ideal model delta sigma weight residual 122.17 116.74 5.43 8.90e-01 1.26e+00 3.72e+01 ... (remaining 198267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.35: 85454 31.35 - 62.70: 2702 62.70 - 94.05: 205 94.05 - 125.41: 7 125.41 - 156.76: 4 Dihedral angle restraints: 88372 sinusoidal: 36168 harmonic: 52204 Sorted by residual: dihedral pdb=" CB CYS C 230 " pdb=" SG CYS C 230 " pdb=" SG CYS C 253 " pdb=" CB CYS C 253 " ideal model delta sinusoidal sigma weight residual 93.00 32.20 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS D 230 " pdb=" SG CYS D 230 " pdb=" SG CYS D 253 " pdb=" CB CYS D 253 " ideal model delta sinusoidal sigma weight residual 93.00 32.20 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual 93.00 32.22 60.78 1 1.00e+01 1.00e-02 4.91e+01 ... (remaining 88369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 20633 0.122 - 0.245: 1128 0.245 - 0.367: 27 0.367 - 0.489: 0 0.489 - 0.611: 4 Chirality restraints: 21792 Sorted by residual: chirality pdb=" CG LEU D4111 " pdb=" CB LEU D4111 " pdb=" CD1 LEU D4111 " pdb=" CD2 LEU D4111 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CG LEU C4111 " pdb=" CB LEU C4111 " pdb=" CD1 LEU C4111 " pdb=" CD2 LEU C4111 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" CG LEU B4111 " pdb=" CB LEU B4111 " pdb=" CD1 LEU B4111 " pdb=" CD2 LEU B4111 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.25e+00 ... (remaining 21789 not shown) Planarity restraints: 25772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D1143 " 0.022 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP D1143 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP D1143 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP D1143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D1143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D1143 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP D1143 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1143 " 0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP D1143 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1143 " -0.021 2.00e-02 2.50e+03 2.74e-02 1.87e+01 pdb=" CG TRP B1143 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP B1143 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B1143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1143 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B1143 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1143 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP B1143 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1143 " -0.021 2.00e-02 2.50e+03 2.73e-02 1.87e+01 pdb=" CG TRP A1143 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP A1143 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A1143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1143 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1143 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A1143 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1143 " -0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A1143 " 0.002 2.00e-02 2.50e+03 ... (remaining 25769 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 6619 2.72 - 3.27: 145352 3.27 - 3.81: 243858 3.81 - 4.36: 294105 4.36 - 4.90: 486471 Nonbonded interactions: 1176405 Sorted by model distance: nonbonded pdb=" OG1 THR D 978 " pdb=" OE1 GLN D 981 " model vdw 2.181 2.440 nonbonded pdb=" OG1 THR A 978 " pdb=" OE1 GLN A 981 " model vdw 2.181 2.440 nonbonded pdb=" OG1 THR C 978 " pdb=" OE1 GLN C 981 " model vdw 2.182 2.440 nonbonded pdb=" OG1 THR B 978 " pdb=" OE1 GLN B 981 " model vdw 2.182 2.440 nonbonded pdb=" OG SER A3752 " pdb=" OE1 GLU A3755 " model vdw 2.240 2.440 ... (remaining 1176400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'B' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'C' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'D' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.190 Extract box with map and model: 18.690 Check model and map are aligned: 1.570 Set scattering table: 1.020 Process input model: 459.740 Find NCS groups from input model: 8.480 Set up NCS constraints: 0.980 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: 0.030 Load rotamer database and sin/cos tables:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 496.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.006 0.089 146364 Z= 0.368 Angle : 1.081 14.673 198272 Z= 0.579 Chirality : 0.061 0.611 21792 Planarity : 0.007 0.058 25772 Dihedral : 14.527 156.758 54640 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 2.77 % Allowed : 2.09 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % 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: -0.30 (0.06), residues: 17844 helix: 0.37 (0.06), residues: 8552 sheet: -0.67 (0.13), residues: 1640 loop : -0.63 (0.07), residues: 7652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP D1143 HIS 0.015 0.002 HIS B3771 PHE 0.039 0.003 PHE C2973 TYR 0.030 0.003 TYR C3166 ARG 0.013 0.001 ARG A3227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1856 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 424 poor density : 1432 time to evaluate : 12.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 37 LEU cc_start: 0.9195 (mt) cc_final: 0.8576 (pt) REVERT: A 116 MET cc_start: 0.9263 (mmm) cc_final: 0.8693 (mmm) REVERT: A 524 GLU cc_start: 0.9430 (mp0) cc_final: 0.9228 (mp0) REVERT: A 846 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7338 (tm) REVERT: A 961 MET cc_start: 0.5258 (pmm) cc_final: 0.4887 (pmm) REVERT: A 1108 GLU cc_start: 0.8505 (mp0) cc_final: 0.8255 (mp0) REVERT: A 1170 MET cc_start: 0.7831 (tpp) cc_final: 0.7528 (tpp) REVERT: A 1286 MET cc_start: 0.5610 (tpt) cc_final: 0.5145 (tpt) REVERT: A 1637 MET cc_start: 0.8903 (ttt) cc_final: 0.8540 (tpp) REVERT: A 1648 MET cc_start: 0.8903 (ptp) cc_final: 0.8346 (pmm) REVERT: A 1713 ASP cc_start: 0.9189 (m-30) cc_final: 0.8920 (t0) REVERT: A 1721 GLU cc_start: 0.8957 (tp30) cc_final: 0.8415 (tp30) REVERT: A 2250 MET cc_start: 0.9292 (mmt) cc_final: 0.9010 (mmm) REVERT: A 2301 TYR cc_start: 0.8884 (m-10) cc_final: 0.8602 (m-10) REVERT: A 2618 MET cc_start: 0.8667 (mpp) cc_final: 0.8108 (mpp) REVERT: A 3435 PHE cc_start: 0.8516 (t80) cc_final: 0.7828 (t80) REVERT: A 3517 MET cc_start: 0.8755 (tpt) cc_final: 0.8383 (tpp) REVERT: A 3518 LEU cc_start: 0.9541 (mt) cc_final: 0.9314 (mt) REVERT: A 3789 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 3999 MET cc_start: 0.9072 (mmm) cc_final: 0.8772 (mmm) REVERT: A 4047 MET cc_start: 0.9300 (tmm) cc_final: 0.9098 (tmm) REVERT: A 4057 MET cc_start: 0.9187 (tpp) cc_final: 0.8851 (tpp) REVERT: A 4229 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8786 (pm20) REVERT: A 4632 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8614 (tt) REVERT: A 4657 CYS cc_start: 0.8874 (m) cc_final: 0.8350 (p) REVERT: A 4809 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: A 4849 TYR cc_start: 0.9162 (t80) cc_final: 0.8949 (t80) REVERT: A 4880 MET cc_start: 0.8751 (tpp) cc_final: 0.8543 (tpp) REVERT: A 4942 GLU cc_start: 0.8551 (tt0) cc_final: 0.8312 (mt-10) REVERT: A 4954 MET cc_start: 0.9347 (tpt) cc_final: 0.9076 (mmm) REVERT: A 4971 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9384 (t) REVERT: A 4976 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: A 5012 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9065 (mmtm) REVERT: A 5013 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8789 (mmm) REVERT: A 5030 LYS cc_start: 0.9519 (ttmt) cc_final: 0.9295 (ttmm) REVERT: A 5032 TYR cc_start: 0.8904 (m-80) cc_final: 0.8675 (m-10) REVERT: A 5035 GLN cc_start: 0.9425 (mt0) cc_final: 0.9103 (mp10) REVERT: B 37 LEU cc_start: 0.9189 (mt) cc_final: 0.8568 (pt) REVERT: B 116 MET cc_start: 0.9373 (mmm) cc_final: 0.8819 (mmm) REVERT: B 127 MET cc_start: 0.8847 (tpp) cc_final: 0.8605 (tmm) REVERT: B 846 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7276 (tm) REVERT: B 961 MET cc_start: 0.5252 (pmm) cc_final: 0.4803 (pmm) REVERT: B 1108 GLU cc_start: 0.8540 (mp0) cc_final: 0.8295 (mp0) REVERT: B 1170 MET cc_start: 0.7841 (tpp) cc_final: 0.7416 (tpp) REVERT: B 1286 MET cc_start: 0.5447 (tpt) cc_final: 0.5146 (tpt) REVERT: B 1637 MET cc_start: 0.8786 (ttt) cc_final: 0.8502 (tpp) REVERT: B 1648 MET cc_start: 0.8807 (ptp) cc_final: 0.8273 (pmm) REVERT: B 1713 ASP cc_start: 0.9190 (m-30) cc_final: 0.8920 (t0) REVERT: B 1721 GLU cc_start: 0.8979 (tp30) cc_final: 0.8422 (tp30) REVERT: B 2250 MET cc_start: 0.9276 (mmt) cc_final: 0.8989 (mmm) REVERT: B 2301 TYR cc_start: 0.8885 (m-10) cc_final: 0.8603 (m-10) REVERT: B 2517 PHE cc_start: 0.9385 (t80) cc_final: 0.9082 (t80) REVERT: B 2618 MET cc_start: 0.8660 (mpp) cc_final: 0.8141 (mpp) REVERT: B 2874 MET cc_start: 0.2729 (mtm) cc_final: 0.2529 (ptm) REVERT: B 3435 PHE cc_start: 0.8514 (t80) cc_final: 0.7806 (t80) REVERT: B 3517 MET cc_start: 0.8779 (tpt) cc_final: 0.8393 (tpp) REVERT: B 3518 LEU cc_start: 0.9525 (mt) cc_final: 0.9282 (mt) REVERT: B 3789 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 3999 MET cc_start: 0.9062 (mmm) cc_final: 0.8759 (mmm) REVERT: B 4047 MET cc_start: 0.9318 (tmm) cc_final: 0.9114 (tmm) REVERT: B 4057 MET cc_start: 0.9193 (tpp) cc_final: 0.8869 (tpp) REVERT: B 4183 ILE cc_start: 0.9787 (OUTLIER) cc_final: 0.9443 (pt) REVERT: B 4190 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9117 (mt) REVERT: B 4191 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8074 (mp0) REVERT: B 4229 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8772 (pm20) REVERT: B 4632 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8638 (tt) REVERT: B 4657 CYS cc_start: 0.9025 (m) cc_final: 0.8814 (m) REVERT: B 4809 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: B 4847 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9164 (p) REVERT: B 4849 TYR cc_start: 0.9162 (t80) cc_final: 0.8889 (t80) REVERT: B 4880 MET cc_start: 0.8852 (tpp) cc_final: 0.8570 (tpp) REVERT: B 4942 GLU cc_start: 0.8613 (tt0) cc_final: 0.8332 (mt-10) REVERT: B 4954 MET cc_start: 0.9365 (tpt) cc_final: 0.9122 (mmm) REVERT: B 4982 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8765 (mt-10) REVERT: B 5012 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9080 (mmtm) REVERT: B 5013 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8822 (mmm) REVERT: C 37 LEU cc_start: 0.9191 (mt) cc_final: 0.8570 (pt) REVERT: C 116 MET cc_start: 0.9373 (mmm) cc_final: 0.8820 (mmm) REVERT: C 127 MET cc_start: 0.8846 (tpp) cc_final: 0.8604 (tmm) REVERT: C 846 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7249 (tm) REVERT: C 961 MET cc_start: 0.5260 (pmm) cc_final: 0.4809 (pmm) REVERT: C 1108 GLU cc_start: 0.8536 (mp0) cc_final: 0.8292 (mp0) REVERT: C 1170 MET cc_start: 0.7840 (tpp) cc_final: 0.7415 (tpp) REVERT: C 1286 MET cc_start: 0.5440 (tpt) cc_final: 0.5140 (tpt) REVERT: C 1637 MET cc_start: 0.8787 (ttt) cc_final: 0.8503 (tpp) REVERT: C 1648 MET cc_start: 0.8804 (ptp) cc_final: 0.8270 (pmm) REVERT: C 1713 ASP cc_start: 0.9190 (m-30) cc_final: 0.8920 (t0) REVERT: C 1721 GLU cc_start: 0.8977 (tp30) cc_final: 0.8421 (tp30) REVERT: C 2250 MET cc_start: 0.9278 (mmt) cc_final: 0.8989 (mmm) REVERT: C 2301 TYR cc_start: 0.8885 (m-10) cc_final: 0.8602 (m-10) REVERT: C 2618 MET cc_start: 0.8659 (mpp) cc_final: 0.8140 (mpp) REVERT: C 2874 MET cc_start: 0.2730 (mtm) cc_final: 0.2528 (ptm) REVERT: C 3435 PHE cc_start: 0.8514 (t80) cc_final: 0.7809 (t80) REVERT: C 3517 MET cc_start: 0.8755 (tpt) cc_final: 0.8364 (tpp) REVERT: C 3518 LEU cc_start: 0.9525 (mt) cc_final: 0.9281 (mt) REVERT: C 3789 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 3999 MET cc_start: 0.9063 (mmm) cc_final: 0.8761 (mmm) REVERT: C 4047 MET cc_start: 0.9315 (tmm) cc_final: 0.9112 (tmm) REVERT: C 4057 MET cc_start: 0.9193 (tpp) cc_final: 0.8868 (tpp) REVERT: C 4183 ILE cc_start: 0.9786 (OUTLIER) cc_final: 0.9442 (pt) REVERT: C 4190 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9121 (mm) REVERT: C 4191 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8079 (mp0) REVERT: C 4229 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8783 (pm20) REVERT: C 4632 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8632 (tt) REVERT: C 4657 CYS cc_start: 0.9025 (m) cc_final: 0.8812 (m) REVERT: C 4809 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: C 4847 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9171 (p) REVERT: C 4849 TYR cc_start: 0.9160 (t80) cc_final: 0.8892 (t80) REVERT: C 4880 MET cc_start: 0.8854 (tpp) cc_final: 0.8617 (tpp) REVERT: C 4942 GLU cc_start: 0.8602 (tt0) cc_final: 0.8346 (mt-10) REVERT: C 4954 MET cc_start: 0.9365 (tpt) cc_final: 0.9121 (mmm) REVERT: C 4982 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8766 (mt-10) REVERT: C 5012 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9081 (mmtm) REVERT: C 5013 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8817 (mmm) REVERT: C 5032 TYR cc_start: 0.8863 (m-80) cc_final: 0.8634 (m-10) REVERT: C 5035 GLN cc_start: 0.9462 (mt0) cc_final: 0.9184 (mp10) REVERT: D 37 LEU cc_start: 0.9191 (mt) cc_final: 0.8571 (pt) REVERT: D 116 MET cc_start: 0.9374 (mmm) cc_final: 0.8803 (mmm) REVERT: D 127 MET cc_start: 0.8847 (tpp) cc_final: 0.8605 (tmm) REVERT: D 846 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7247 (tm) REVERT: D 961 MET cc_start: 0.5259 (pmm) cc_final: 0.4811 (pmm) REVERT: D 1108 GLU cc_start: 0.8536 (mp0) cc_final: 0.8291 (mp0) REVERT: D 1170 MET cc_start: 0.7836 (tpp) cc_final: 0.7406 (tpp) REVERT: D 1286 MET cc_start: 0.5442 (tpt) cc_final: 0.5141 (tpt) REVERT: D 1637 MET cc_start: 0.8787 (ttt) cc_final: 0.8502 (tpp) REVERT: D 1648 MET cc_start: 0.8804 (ptp) cc_final: 0.8270 (pmm) REVERT: D 1713 ASP cc_start: 0.9191 (m-30) cc_final: 0.8919 (t0) REVERT: D 1721 GLU cc_start: 0.8978 (tp30) cc_final: 0.8422 (tp30) REVERT: D 2250 MET cc_start: 0.9277 (mmt) cc_final: 0.8991 (mmm) REVERT: D 2301 TYR cc_start: 0.8886 (m-10) cc_final: 0.8605 (m-10) REVERT: D 2517 PHE cc_start: 0.9385 (t80) cc_final: 0.9080 (t80) REVERT: D 2618 MET cc_start: 0.8663 (mpp) cc_final: 0.8145 (mpp) REVERT: D 2874 MET cc_start: 0.2731 (mtm) cc_final: 0.2529 (ptm) REVERT: D 3435 PHE cc_start: 0.8518 (t80) cc_final: 0.7817 (t80) REVERT: D 3517 MET cc_start: 0.8759 (tpt) cc_final: 0.8366 (tpp) REVERT: D 3518 LEU cc_start: 0.9526 (mt) cc_final: 0.9283 (mt) REVERT: D 3789 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8206 (tm-30) REVERT: D 3999 MET cc_start: 0.9063 (mmm) cc_final: 0.8761 (mmm) REVERT: D 4057 MET cc_start: 0.9192 (tpp) cc_final: 0.8861 (tpp) REVERT: D 4183 ILE cc_start: 0.9787 (OUTLIER) cc_final: 0.9440 (pt) REVERT: D 4190 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9123 (mm) REVERT: D 4191 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8079 (mp0) REVERT: D 4229 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8780 (pm20) REVERT: D 4632 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (tt) REVERT: D 4657 CYS cc_start: 0.9029 (m) cc_final: 0.8819 (m) REVERT: D 4809 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: D 4847 VAL cc_start: 0.9430 (OUTLIER) cc_final: 0.9168 (p) REVERT: D 4849 TYR cc_start: 0.9163 (t80) cc_final: 0.8901 (t80) REVERT: D 4880 MET cc_start: 0.8862 (tpp) cc_final: 0.8622 (tpp) REVERT: D 4942 GLU cc_start: 0.8607 (tt0) cc_final: 0.8351 (mt-10) REVERT: D 4954 MET cc_start: 0.9365 (tpt) cc_final: 0.9122 (mmm) REVERT: D 4982 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8765 (mt-10) REVERT: D 5012 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9078 (mmtm) REVERT: D 5013 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8819 (mmm) REVERT: E 29 MET cc_start: 0.9004 (mtp) cc_final: 0.8547 (ttp) REVERT: F 29 MET cc_start: 0.9003 (mtp) cc_final: 0.8548 (ttp) REVERT: G 29 MET cc_start: 0.9003 (mtp) cc_final: 0.8546 (ttp) REVERT: H 29 MET cc_start: 0.9004 (mtp) cc_final: 0.8546 (ttp) outliers start: 424 outliers final: 76 residues processed: 1735 average time/residue: 1.2164 time to fit residues: 3760.8972 Evaluate side-chains 1074 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 960 time to evaluate : 12.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4188 ARG Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4229 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4632 LEU Chi-restraints excluded: chain A residue 4635 SER Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4809 PHE Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4927 ILE Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4976 GLU Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain A residue 5012 LYS Chi-restraints excluded: chain A residue 5013 MET Chi-restraints excluded: chain A residue 5015 GLN Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4188 ARG Chi-restraints excluded: chain B residue 4190 ILE Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4229 GLU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4632 LEU Chi-restraints excluded: chain B residue 4635 SER Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4809 PHE Chi-restraints excluded: chain B residue 4843 LEU Chi-restraints excluded: chain B residue 4847 VAL Chi-restraints excluded: chain B residue 4927 ILE Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4982 GLU Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain B residue 5012 LYS Chi-restraints excluded: chain B residue 5013 MET Chi-restraints excluded: chain B residue 5015 GLN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4188 ARG Chi-restraints excluded: chain C residue 4190 ILE Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4229 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4632 LEU Chi-restraints excluded: chain C residue 4635 SER Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4809 PHE Chi-restraints excluded: chain C residue 4843 LEU Chi-restraints excluded: chain C residue 4847 VAL Chi-restraints excluded: chain C residue 4927 ILE Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4982 GLU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain C residue 5012 LYS Chi-restraints excluded: chain C residue 5013 MET Chi-restraints excluded: chain C residue 5015 GLN Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4188 ARG Chi-restraints excluded: chain D residue 4190 ILE Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4229 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4632 LEU Chi-restraints excluded: chain D residue 4635 SER Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4809 PHE Chi-restraints excluded: chain D residue 4843 LEU Chi-restraints excluded: chain D residue 4847 VAL Chi-restraints excluded: chain D residue 4927 ILE Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4982 GLU Chi-restraints excluded: chain D residue 4993 MET Chi-restraints excluded: chain D residue 5012 LYS Chi-restraints excluded: chain D residue 5013 MET Chi-restraints excluded: chain D residue 5015 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 0.8980 chunk 1355 optimal weight: 3.9990 chunk 751 optimal weight: 6.9990 chunk 462 optimal weight: 9.9990 chunk 914 optimal weight: 0.6980 chunk 724 optimal weight: 30.0000 chunk 1401 optimal weight: 6.9990 chunk 542 optimal weight: 5.9990 chunk 852 optimal weight: 0.2980 chunk 1043 optimal weight: 3.9990 chunk 1623 optimal weight: 40.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS A 624 ASN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN A1460 HIS A1631 GLN A2127 GLN A2173 GLN ** A2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN A2444 GLN ** A2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4201 ASN A4626 ASN A4949 GLN A5003 HIS A5031 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS B 624 ASN ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 HIS B 994 ASN B1299 GLN B1460 HIS B1631 GLN B2127 GLN B2173 GLN ** B2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN B2444 GLN ** B2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4201 ASN B4626 ASN B4949 GLN B5003 HIS B5031 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 HIS C 624 ASN ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 994 ASN C1299 GLN C1460 HIS C1631 GLN C2127 GLN C2173 GLN ** C2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN C2444 GLN ** C2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4201 ASN C4626 ASN C4949 GLN C5003 HIS C5031 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 HIS D 624 ASN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 ASN D1299 GLN D1460 HIS D1631 GLN D2127 GLN D2173 GLN ** D2246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2247 GLN D2444 GLN ** D2872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4201 ASN D4626 ASN D4949 GLN D5003 HIS D5031 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 146364 Z= 0.193 Angle : 0.676 14.867 198272 Z= 0.338 Chirality : 0.043 0.281 21792 Planarity : 0.004 0.062 25772 Dihedral : 6.385 149.833 19860 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.38 % Allowed : 7.58 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.32 (0.06), residues: 17844 helix: 1.05 (0.06), residues: 8684 sheet: -0.50 (0.14), residues: 1548 loop : -0.53 (0.07), residues: 7612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D1143 HIS 0.009 0.001 HIS B3771 PHE 0.044 0.001 PHE B3552 TYR 0.023 0.001 TYR D3968 ARG 0.011 0.000 ARG A4189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1030 time to evaluate : 12.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.9360 (mmm) cc_final: 0.8566 (tmm) REVERT: A 524 GLU cc_start: 0.9286 (mp0) cc_final: 0.9060 (mp0) REVERT: A 846 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7305 (tm) REVERT: A 941 MET cc_start: 0.7082 (tpt) cc_final: 0.6806 (tpt) REVERT: A 961 MET cc_start: 0.4804 (pmm) cc_final: 0.4517 (pmm) REVERT: A 1170 MET cc_start: 0.7631 (tpp) cc_final: 0.7242 (tpp) REVERT: A 1186 ASP cc_start: 0.8612 (p0) cc_final: 0.8355 (p0) REVERT: A 1286 MET cc_start: 0.5939 (tpt) cc_final: 0.5581 (tpt) REVERT: A 1637 MET cc_start: 0.8880 (ttt) cc_final: 0.8564 (tpp) REVERT: A 1639 LEU cc_start: 0.9111 (tt) cc_final: 0.8311 (tt) REVERT: A 1648 MET cc_start: 0.8866 (ptp) cc_final: 0.8340 (pmm) REVERT: A 1721 GLU cc_start: 0.9011 (tp30) cc_final: 0.8388 (tp30) REVERT: A 2211 MET cc_start: 0.9235 (mmm) cc_final: 0.8881 (mmm) REVERT: A 2267 MET cc_start: 0.7557 (tmm) cc_final: 0.7273 (tmm) REVERT: A 2292 GLU cc_start: 0.9449 (pm20) cc_final: 0.9126 (pm20) REVERT: A 2301 TYR cc_start: 0.8828 (m-10) cc_final: 0.8551 (m-10) REVERT: A 2444 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.9159 (mp10) REVERT: A 2546 MET cc_start: 0.8070 (mmm) cc_final: 0.7627 (mmm) REVERT: A 2618 MET cc_start: 0.8686 (mpp) cc_final: 0.8110 (mpp) REVERT: A 3435 PHE cc_start: 0.8606 (t80) cc_final: 0.7847 (t80) REVERT: A 3518 LEU cc_start: 0.9578 (mt) cc_final: 0.9178 (mt) REVERT: A 3652 MET cc_start: 0.9303 (pmm) cc_final: 0.9089 (pmm) REVERT: A 3720 TYR cc_start: 0.8263 (p90) cc_final: 0.8026 (p90) REVERT: A 3789 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8164 (pp20) REVERT: A 3999 MET cc_start: 0.9139 (mmm) cc_final: 0.8930 (mmm) REVERT: A 4017 LEU cc_start: 0.9567 (mt) cc_final: 0.9259 (pp) REVERT: A 4191 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8042 (mp0) REVERT: A 4657 CYS cc_start: 0.8874 (m) cc_final: 0.8267 (p) REVERT: A 4743 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8010 (ptm) REVERT: A 4874 MET cc_start: 0.9140 (mmm) cc_final: 0.8760 (mmm) REVERT: A 4880 MET cc_start: 0.8923 (tpp) cc_final: 0.8692 (tpp) REVERT: A 4942 GLU cc_start: 0.8626 (tt0) cc_final: 0.8347 (mt-10) REVERT: A 4953 ASP cc_start: 0.9014 (m-30) cc_final: 0.8636 (m-30) REVERT: A 4954 MET cc_start: 0.9429 (tpt) cc_final: 0.9145 (mmm) REVERT: A 4993 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8282 (ttt) REVERT: A 5013 MET cc_start: 0.9097 (mtp) cc_final: 0.8794 (mtp) REVERT: A 5030 LYS cc_start: 0.9514 (ttmt) cc_final: 0.9309 (ttmm) REVERT: A 5032 TYR cc_start: 0.9047 (m-80) cc_final: 0.8559 (m-10) REVERT: A 5035 GLN cc_start: 0.9429 (mt0) cc_final: 0.8966 (mp10) REVERT: B 116 MET cc_start: 0.9387 (mmm) cc_final: 0.8600 (tmm) REVERT: B 127 MET cc_start: 0.8764 (tpp) cc_final: 0.8524 (tmm) REVERT: B 846 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7057 (tm) REVERT: B 941 MET cc_start: 0.7211 (tpt) cc_final: 0.6940 (tpt) REVERT: B 961 MET cc_start: 0.4825 (pmm) cc_final: 0.4499 (pmm) REVERT: B 1170 MET cc_start: 0.7818 (tpp) cc_final: 0.7436 (tpp) REVERT: B 1286 MET cc_start: 0.5675 (tpt) cc_final: 0.5396 (tpt) REVERT: B 1637 MET cc_start: 0.8811 (ttt) cc_final: 0.8576 (tpp) REVERT: B 1648 MET cc_start: 0.8845 (ptp) cc_final: 0.8335 (pmm) REVERT: B 1721 GLU cc_start: 0.9017 (tp30) cc_final: 0.8484 (tp30) REVERT: B 2211 MET cc_start: 0.9223 (mmm) cc_final: 0.8888 (mmm) REVERT: B 2267 MET cc_start: 0.7598 (tmm) cc_final: 0.7315 (tmm) REVERT: B 2292 GLU cc_start: 0.9477 (pm20) cc_final: 0.9139 (pm20) REVERT: B 2301 TYR cc_start: 0.8864 (m-10) cc_final: 0.8592 (m-10) REVERT: B 2444 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.9158 (mp10) REVERT: B 2517 PHE cc_start: 0.9306 (t80) cc_final: 0.9066 (t80) REVERT: B 2618 MET cc_start: 0.8682 (mpp) cc_final: 0.8105 (mpp) REVERT: B 3435 PHE cc_start: 0.8584 (t80) cc_final: 0.7872 (t80) REVERT: B 3517 MET cc_start: 0.8906 (tpt) cc_final: 0.8676 (tpp) REVERT: B 3518 LEU cc_start: 0.9587 (mt) cc_final: 0.9263 (mt) REVERT: B 3652 MET cc_start: 0.9309 (pmm) cc_final: 0.9083 (pmm) REVERT: B 3789 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8176 (pp20) REVERT: B 3968 TYR cc_start: 0.8702 (m-10) cc_final: 0.8487 (m-10) REVERT: B 4183 ILE cc_start: 0.9793 (OUTLIER) cc_final: 0.9534 (pt) REVERT: B 4191 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8056 (mp0) REVERT: B 4244 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8988 (mm-30) REVERT: B 4657 CYS cc_start: 0.8888 (m) cc_final: 0.8612 (m) REVERT: B 4849 TYR cc_start: 0.9243 (t80) cc_final: 0.9031 (t80) REVERT: B 4874 MET cc_start: 0.9232 (mmt) cc_final: 0.9028 (mmm) REVERT: B 4880 MET cc_start: 0.9005 (tpp) cc_final: 0.8722 (mmm) REVERT: B 4942 GLU cc_start: 0.8666 (tt0) cc_final: 0.8373 (mt-10) REVERT: B 4953 ASP cc_start: 0.9058 (m-30) cc_final: 0.8692 (m-30) REVERT: B 4954 MET cc_start: 0.9449 (tpt) cc_final: 0.9173 (mmm) REVERT: B 4993 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8259 (ttt) REVERT: B 5012 LYS cc_start: 0.9400 (mptt) cc_final: 0.9134 (mmtm) REVERT: B 5013 MET cc_start: 0.9124 (mtp) cc_final: 0.8805 (mtp) REVERT: B 5035 GLN cc_start: 0.9476 (mt0) cc_final: 0.8993 (mp10) REVERT: C 116 MET cc_start: 0.9388 (mmm) cc_final: 0.8601 (tmm) REVERT: C 127 MET cc_start: 0.8765 (tpp) cc_final: 0.8524 (tmm) REVERT: C 846 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7060 (tm) REVERT: C 941 MET cc_start: 0.7207 (tpt) cc_final: 0.6936 (tpt) REVERT: C 961 MET cc_start: 0.4826 (pmm) cc_final: 0.4499 (pmm) REVERT: C 1170 MET cc_start: 0.7815 (tpp) cc_final: 0.7432 (tpp) REVERT: C 1286 MET cc_start: 0.5672 (tpt) cc_final: 0.5392 (tpt) REVERT: C 1637 MET cc_start: 0.8814 (ttt) cc_final: 0.8575 (tpp) REVERT: C 1648 MET cc_start: 0.8844 (ptp) cc_final: 0.8329 (pmm) REVERT: C 1721 GLU cc_start: 0.9015 (tp30) cc_final: 0.8482 (tp30) REVERT: C 2211 MET cc_start: 0.9225 (mmm) cc_final: 0.8890 (mmm) REVERT: C 2267 MET cc_start: 0.7596 (tmm) cc_final: 0.7316 (tmm) REVERT: C 2292 GLU cc_start: 0.9457 (pm20) cc_final: 0.9140 (pm20) REVERT: C 2301 TYR cc_start: 0.8865 (m-10) cc_final: 0.8593 (m-10) REVERT: C 2444 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.9160 (mp10) REVERT: C 2618 MET cc_start: 0.8683 (mpp) cc_final: 0.8107 (mpp) REVERT: C 3435 PHE cc_start: 0.8583 (t80) cc_final: 0.7871 (t80) REVERT: C 3517 MET cc_start: 0.8899 (tpt) cc_final: 0.8676 (tpp) REVERT: C 3518 LEU cc_start: 0.9586 (mt) cc_final: 0.9263 (mt) REVERT: C 3652 MET cc_start: 0.9308 (pmm) cc_final: 0.9083 (pmm) REVERT: C 3720 TYR cc_start: 0.8301 (p90) cc_final: 0.8077 (p90) REVERT: C 3789 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8176 (pp20) REVERT: C 3968 TYR cc_start: 0.8701 (m-10) cc_final: 0.8485 (m-10) REVERT: C 4183 ILE cc_start: 0.9792 (OUTLIER) cc_final: 0.9534 (pt) REVERT: C 4191 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8061 (mp0) REVERT: C 4244 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8987 (mm-30) REVERT: C 4657 CYS cc_start: 0.8891 (m) cc_final: 0.8613 (m) REVERT: C 4849 TYR cc_start: 0.9241 (t80) cc_final: 0.9032 (t80) REVERT: C 4874 MET cc_start: 0.9233 (mmt) cc_final: 0.9012 (mmm) REVERT: C 4880 MET cc_start: 0.9005 (tpp) cc_final: 0.8744 (mmm) REVERT: C 4942 GLU cc_start: 0.8654 (tt0) cc_final: 0.8384 (mt-10) REVERT: C 4953 ASP cc_start: 0.9055 (m-30) cc_final: 0.8692 (m-30) REVERT: C 4954 MET cc_start: 0.9447 (tpt) cc_final: 0.9171 (mmm) REVERT: C 4993 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8261 (ttt) REVERT: C 5012 LYS cc_start: 0.9400 (mptt) cc_final: 0.9136 (mmtm) REVERT: C 5013 MET cc_start: 0.9127 (mtp) cc_final: 0.8804 (mtp) REVERT: C 5032 TYR cc_start: 0.9052 (m-80) cc_final: 0.8543 (m-10) REVERT: C 5035 GLN cc_start: 0.9472 (mt0) cc_final: 0.9006 (mp10) REVERT: D 116 MET cc_start: 0.9389 (mmm) cc_final: 0.8603 (tmm) REVERT: D 127 MET cc_start: 0.8764 (tpp) cc_final: 0.8524 (tmm) REVERT: D 846 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7061 (tm) REVERT: D 941 MET cc_start: 0.7206 (tpt) cc_final: 0.6935 (tpt) REVERT: D 961 MET cc_start: 0.4831 (pmm) cc_final: 0.4502 (pmm) REVERT: D 1170 MET cc_start: 0.7818 (tpp) cc_final: 0.7434 (tpp) REVERT: D 1286 MET cc_start: 0.5671 (tpt) cc_final: 0.5391 (tpt) REVERT: D 1637 MET cc_start: 0.8812 (ttt) cc_final: 0.8574 (tpp) REVERT: D 1648 MET cc_start: 0.8844 (ptp) cc_final: 0.8331 (pmm) REVERT: D 1721 GLU cc_start: 0.9015 (tp30) cc_final: 0.8483 (tp30) REVERT: D 2211 MET cc_start: 0.9225 (mmm) cc_final: 0.8888 (mmm) REVERT: D 2267 MET cc_start: 0.7598 (tmm) cc_final: 0.7318 (tmm) REVERT: D 2292 GLU cc_start: 0.9457 (pm20) cc_final: 0.9140 (pm20) REVERT: D 2301 TYR cc_start: 0.8865 (m-10) cc_final: 0.8595 (m-10) REVERT: D 2444 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.9159 (mp10) REVERT: D 2517 PHE cc_start: 0.9305 (t80) cc_final: 0.9060 (t80) REVERT: D 2618 MET cc_start: 0.8683 (mpp) cc_final: 0.8106 (mpp) REVERT: D 3435 PHE cc_start: 0.8585 (t80) cc_final: 0.7875 (t80) REVERT: D 3517 MET cc_start: 0.8920 (tpt) cc_final: 0.8699 (tpp) REVERT: D 3518 LEU cc_start: 0.9587 (mt) cc_final: 0.9264 (mt) REVERT: D 3652 MET cc_start: 0.9310 (pmm) cc_final: 0.9085 (pmm) REVERT: D 3789 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8178 (pp20) REVERT: D 3968 TYR cc_start: 0.8700 (m-10) cc_final: 0.8481 (m-10) REVERT: D 3999 MET cc_start: 0.9133 (mmm) cc_final: 0.8933 (mmm) REVERT: D 4183 ILE cc_start: 0.9793 (OUTLIER) cc_final: 0.9533 (pt) REVERT: D 4191 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8057 (mp0) REVERT: D 4244 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8981 (mm-30) REVERT: D 4657 CYS cc_start: 0.8890 (m) cc_final: 0.8619 (m) REVERT: D 4849 TYR cc_start: 0.9244 (t80) cc_final: 0.9037 (t80) REVERT: D 4874 MET cc_start: 0.9240 (mmt) cc_final: 0.9027 (mmm) REVERT: D 4880 MET cc_start: 0.9014 (tpp) cc_final: 0.8753 (mmm) REVERT: D 4942 GLU cc_start: 0.8662 (tt0) cc_final: 0.8396 (mt-10) REVERT: D 4949 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7625 (tp40) REVERT: D 4953 ASP cc_start: 0.9116 (m-30) cc_final: 0.8526 (m-30) REVERT: D 4954 MET cc_start: 0.9442 (tpt) cc_final: 0.9131 (mmm) REVERT: D 4993 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8265 (ttt) REVERT: D 5012 LYS cc_start: 0.9397 (mptt) cc_final: 0.9134 (mmtm) REVERT: D 5013 MET cc_start: 0.9125 (mtp) cc_final: 0.8804 (mtp) REVERT: D 5035 GLN cc_start: 0.9477 (mt0) cc_final: 0.8992 (mp10) REVERT: E 29 MET cc_start: 0.8946 (mtp) cc_final: 0.8548 (ttp) REVERT: F 29 MET cc_start: 0.8944 (mtp) cc_final: 0.8547 (ttp) REVERT: G 29 MET cc_start: 0.8944 (mtp) cc_final: 0.8545 (ttp) REVERT: H 29 MET cc_start: 0.8942 (mtp) cc_final: 0.8546 (ttp) outliers start: 203 outliers final: 109 residues processed: 1181 average time/residue: 1.1643 time to fit residues: 2503.5204 Evaluate side-chains 1058 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 932 time to evaluate : 12.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1958 LEU Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2444 GLN Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4556 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4635 SER Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4884 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4927 ILE Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain A residue 4995 LEU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 1958 LEU Chi-restraints excluded: chain B residue 2170 MET Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2444 GLN Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4635 SER Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4706 LEU Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4927 ILE Chi-restraints excluded: chain B residue 4931 ILE Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 98 HIS Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 1958 LEU Chi-restraints excluded: chain C residue 2170 MET Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2444 GLN Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4635 SER Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4706 LEU Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4927 ILE Chi-restraints excluded: chain C residue 4931 ILE Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 98 HIS Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 1958 LEU Chi-restraints excluded: chain D residue 2170 MET Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2444 GLN Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4635 SER Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4706 LEU Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4927 ILE Chi-restraints excluded: chain D residue 4931 ILE Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4949 GLN Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 0.3980 chunk 503 optimal weight: 2.9990 chunk 1351 optimal weight: 6.9990 chunk 1105 optimal weight: 6.9990 chunk 447 optimal weight: 8.9990 chunk 1626 optimal weight: 30.0000 chunk 1757 optimal weight: 8.9990 chunk 1448 optimal weight: 50.0000 chunk 1613 optimal weight: 0.9980 chunk 554 optimal weight: 10.0000 chunk 1304 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 GLN A2127 GLN A2487 GLN ** A2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3128 ASN A3895 HIS ** A4700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 GLN B2127 GLN B2260 ASN B2487 GLN B3608 GLN B3895 HIS B4886 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1041 GLN C2127 GLN C2260 ASN C2487 GLN ** C2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3128 ASN C3895 HIS C4886 HIS ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1041 GLN D2127 GLN D2260 ASN D2487 GLN D3128 ASN D3895 HIS D4886 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 146364 Z= 0.229 Angle : 0.656 14.437 198272 Z= 0.328 Chirality : 0.042 0.259 21792 Planarity : 0.004 0.063 25772 Dihedral : 5.753 149.650 19726 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.39 % Allowed : 9.48 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.41 (0.06), residues: 17844 helix: 1.16 (0.06), residues: 8732 sheet: -0.56 (0.13), residues: 1608 loop : -0.52 (0.07), residues: 7504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A4644 HIS 0.013 0.001 HIS B 904 PHE 0.041 0.002 PHE D3552 TYR 0.029 0.001 TYR A3968 ARG 0.007 0.000 ARG A4189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 956 time to evaluate : 12.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.9345 (mmm) cc_final: 0.8334 (tmm) REVERT: A 226 HIS cc_start: 0.8913 (m-70) cc_final: 0.8708 (m-70) REVERT: A 846 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7284 (tm) REVERT: A 941 MET cc_start: 0.7089 (tpt) cc_final: 0.6808 (tpt) REVERT: A 1170 MET cc_start: 0.7749 (tpp) cc_final: 0.7426 (tpp) REVERT: A 1286 MET cc_start: 0.5776 (tpt) cc_final: 0.5533 (tpt) REVERT: A 2203 MET cc_start: 0.9317 (ptp) cc_final: 0.9037 (mpp) REVERT: A 2211 MET cc_start: 0.9247 (mmm) cc_final: 0.8897 (mmm) REVERT: A 2250 MET cc_start: 0.9191 (mmm) cc_final: 0.8489 (mmm) REVERT: A 2301 TYR cc_start: 0.8892 (m-10) cc_final: 0.8519 (m-10) REVERT: A 2530 MET cc_start: 0.8709 (ppp) cc_final: 0.8218 (ppp) REVERT: A 2618 MET cc_start: 0.8722 (mpp) cc_final: 0.8080 (mpp) REVERT: A 3038 MET cc_start: 0.5791 (ppp) cc_final: 0.4318 (ptm) REVERT: A 3106 MET cc_start: 0.8848 (mmm) cc_final: 0.8526 (mmm) REVERT: A 3435 PHE cc_start: 0.8535 (t80) cc_final: 0.7738 (t80) REVERT: A 3437 MET cc_start: 0.9032 (mpp) cc_final: 0.8192 (mtt) REVERT: A 3517 MET cc_start: 0.8716 (tpp) cc_final: 0.8455 (tpp) REVERT: A 3518 LEU cc_start: 0.9547 (mt) cc_final: 0.9238 (mt) REVERT: A 3789 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8270 (pp20) REVERT: A 4017 LEU cc_start: 0.9600 (mt) cc_final: 0.9307 (pp) REVERT: A 4107 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6785 (tp30) REVERT: A 4178 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9212 (tt) REVERT: A 4874 MET cc_start: 0.9202 (mmm) cc_final: 0.8856 (mmm) REVERT: A 4880 MET cc_start: 0.9033 (tpp) cc_final: 0.8795 (tpp) REVERT: A 4942 GLU cc_start: 0.8655 (tt0) cc_final: 0.8414 (mt-10) REVERT: A 4953 ASP cc_start: 0.8984 (m-30) cc_final: 0.8636 (m-30) REVERT: A 4954 MET cc_start: 0.9442 (tpt) cc_final: 0.9185 (mmm) REVERT: A 4965 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (m) REVERT: A 4993 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8416 (ttp) REVERT: A 5012 LYS cc_start: 0.9391 (mptt) cc_final: 0.9159 (mmtm) REVERT: A 5013 MET cc_start: 0.9047 (mtp) cc_final: 0.8683 (mmm) REVERT: A 5030 LYS cc_start: 0.9564 (ttmt) cc_final: 0.9345 (ttmm) REVERT: A 5032 TYR cc_start: 0.9112 (m-80) cc_final: 0.8803 (m-10) REVERT: A 5035 GLN cc_start: 0.9445 (mt0) cc_final: 0.8986 (mp10) REVERT: B 116 MET cc_start: 0.9368 (mmm) cc_final: 0.8838 (mmm) REVERT: B 127 MET cc_start: 0.8841 (tpp) cc_final: 0.8576 (tmm) REVERT: B 846 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7081 (tm) REVERT: B 941 MET cc_start: 0.7242 (tpt) cc_final: 0.6979 (tpt) REVERT: B 1170 MET cc_start: 0.7831 (tpp) cc_final: 0.7517 (tpp) REVERT: B 1186 ASP cc_start: 0.8568 (p0) cc_final: 0.8340 (p0) REVERT: B 1286 MET cc_start: 0.5790 (tpt) cc_final: 0.5527 (tpt) REVERT: B 1637 MET cc_start: 0.8826 (ttt) cc_final: 0.8568 (tpp) REVERT: B 1648 MET cc_start: 0.8856 (ptp) cc_final: 0.8357 (pmm) REVERT: B 2203 MET cc_start: 0.9307 (ptp) cc_final: 0.9062 (mpp) REVERT: B 2211 MET cc_start: 0.9240 (mmm) cc_final: 0.8854 (mmm) REVERT: B 2250 MET cc_start: 0.9235 (mmm) cc_final: 0.8503 (mmm) REVERT: B 2301 TYR cc_start: 0.8884 (m-10) cc_final: 0.8504 (m-10) REVERT: B 2517 PHE cc_start: 0.9329 (t80) cc_final: 0.9030 (t80) REVERT: B 2530 MET cc_start: 0.8700 (ppp) cc_final: 0.8202 (ppp) REVERT: B 2618 MET cc_start: 0.8712 (mpp) cc_final: 0.8077 (mpp) REVERT: B 2874 MET cc_start: -0.5125 (ppp) cc_final: -0.5411 (ptm) REVERT: B 3038 MET cc_start: 0.5927 (ppp) cc_final: 0.4298 (ptm) REVERT: B 3106 MET cc_start: 0.8835 (mmm) cc_final: 0.8511 (mmm) REVERT: B 3435 PHE cc_start: 0.8663 (t80) cc_final: 0.7933 (t80) REVERT: B 3517 MET cc_start: 0.8706 (tpt) cc_final: 0.8499 (tpp) REVERT: B 3518 LEU cc_start: 0.9612 (mt) cc_final: 0.9287 (mt) REVERT: B 3789 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8177 (pp20) REVERT: B 3999 MET cc_start: 0.8859 (mmm) cc_final: 0.8601 (mmm) REVERT: B 4107 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: B 4178 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9172 (tt) REVERT: B 4191 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7988 (mm-30) REVERT: B 4231 MET cc_start: 0.9374 (mmm) cc_final: 0.9060 (mmp) REVERT: B 4657 CYS cc_start: 0.8976 (m) cc_final: 0.8652 (m) REVERT: B 4880 MET cc_start: 0.9050 (tpp) cc_final: 0.8773 (tpp) REVERT: B 4933 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8586 (mp10) REVERT: B 4942 GLU cc_start: 0.8685 (tt0) cc_final: 0.8407 (mt-10) REVERT: B 4948 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 4953 ASP cc_start: 0.9046 (m-30) cc_final: 0.8722 (m-30) REVERT: B 4954 MET cc_start: 0.9446 (tpt) cc_final: 0.9205 (mmm) REVERT: B 4993 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8444 (ttp) REVERT: B 5012 LYS cc_start: 0.9395 (mptt) cc_final: 0.9146 (mmtm) REVERT: B 5013 MET cc_start: 0.9053 (mtp) cc_final: 0.8679 (mmm) REVERT: B 5035 GLN cc_start: 0.9487 (mt0) cc_final: 0.8989 (mp10) REVERT: C 116 MET cc_start: 0.9369 (mmm) cc_final: 0.8830 (mmm) REVERT: C 127 MET cc_start: 0.8840 (tpp) cc_final: 0.8575 (tmm) REVERT: C 226 HIS cc_start: 0.8915 (m-70) cc_final: 0.8707 (m-70) REVERT: C 846 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7084 (tm) REVERT: C 941 MET cc_start: 0.7183 (tpt) cc_final: 0.6926 (tpt) REVERT: C 1170 MET cc_start: 0.7828 (tpp) cc_final: 0.7512 (tpp) REVERT: C 1186 ASP cc_start: 0.8567 (p0) cc_final: 0.8339 (p0) REVERT: C 1286 MET cc_start: 0.5789 (tpt) cc_final: 0.5529 (tpt) REVERT: C 1637 MET cc_start: 0.8826 (ttt) cc_final: 0.8570 (tpp) REVERT: C 2203 MET cc_start: 0.9307 (ptp) cc_final: 0.9064 (mpp) REVERT: C 2211 MET cc_start: 0.9242 (mmm) cc_final: 0.8856 (mmm) REVERT: C 2250 MET cc_start: 0.9235 (mmm) cc_final: 0.8500 (mmm) REVERT: C 2301 TYR cc_start: 0.8886 (m-10) cc_final: 0.8505 (m-10) REVERT: C 2530 MET cc_start: 0.8703 (ppp) cc_final: 0.8206 (ppp) REVERT: C 2618 MET cc_start: 0.8714 (mpp) cc_final: 0.8079 (mpp) REVERT: C 2874 MET cc_start: -0.5126 (ppp) cc_final: -0.5413 (ptm) REVERT: C 3038 MET cc_start: 0.5923 (ppp) cc_final: 0.4292 (ptm) REVERT: C 3106 MET cc_start: 0.8833 (mmm) cc_final: 0.8509 (mmm) REVERT: C 3435 PHE cc_start: 0.8663 (t80) cc_final: 0.7935 (t80) REVERT: C 3517 MET cc_start: 0.8706 (tpt) cc_final: 0.8499 (tpp) REVERT: C 3518 LEU cc_start: 0.9612 (mt) cc_final: 0.9287 (mt) REVERT: C 3720 TYR cc_start: 0.8342 (p90) cc_final: 0.8091 (p90) REVERT: C 3789 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8180 (pp20) REVERT: C 3999 MET cc_start: 0.8855 (mmm) cc_final: 0.8602 (mmm) REVERT: C 4107 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6807 (tp30) REVERT: C 4178 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9172 (tt) REVERT: C 4191 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7995 (mm-30) REVERT: C 4657 CYS cc_start: 0.8979 (m) cc_final: 0.8650 (m) REVERT: C 4880 MET cc_start: 0.9049 (tpp) cc_final: 0.8791 (tpp) REVERT: C 4933 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: C 4942 GLU cc_start: 0.8676 (tt0) cc_final: 0.8415 (mt-10) REVERT: C 4953 ASP cc_start: 0.9023 (m-30) cc_final: 0.8683 (m-30) REVERT: C 4954 MET cc_start: 0.9445 (tpt) cc_final: 0.9202 (mmm) REVERT: C 4965 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8889 (m) REVERT: C 4993 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8466 (ttp) REVERT: C 5012 LYS cc_start: 0.9396 (mptt) cc_final: 0.9147 (mmtm) REVERT: C 5013 MET cc_start: 0.9060 (mtp) cc_final: 0.8680 (mmm) REVERT: C 5032 TYR cc_start: 0.9094 (m-80) cc_final: 0.8779 (m-10) REVERT: C 5035 GLN cc_start: 0.9481 (mt0) cc_final: 0.9024 (mp10) REVERT: D 116 MET cc_start: 0.9368 (mmm) cc_final: 0.8829 (mmm) REVERT: D 127 MET cc_start: 0.8839 (tpp) cc_final: 0.8574 (tmm) REVERT: D 226 HIS cc_start: 0.8914 (m-70) cc_final: 0.8701 (m-70) REVERT: D 846 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7084 (tm) REVERT: D 941 MET cc_start: 0.7182 (tpt) cc_final: 0.6925 (tpt) REVERT: D 1170 MET cc_start: 0.7831 (tpp) cc_final: 0.7500 (tpp) REVERT: D 1186 ASP cc_start: 0.8569 (p0) cc_final: 0.8340 (p0) REVERT: D 1286 MET cc_start: 0.5788 (tpt) cc_final: 0.5529 (tpt) REVERT: D 1637 MET cc_start: 0.8826 (ttt) cc_final: 0.8567 (tpp) REVERT: D 2203 MET cc_start: 0.9307 (ptp) cc_final: 0.9064 (mpp) REVERT: D 2211 MET cc_start: 0.9243 (mmm) cc_final: 0.8857 (mmm) REVERT: D 2250 MET cc_start: 0.9236 (mmm) cc_final: 0.8502 (mmm) REVERT: D 2301 TYR cc_start: 0.8885 (m-10) cc_final: 0.8506 (m-10) REVERT: D 2517 PHE cc_start: 0.9323 (t80) cc_final: 0.9041 (t80) REVERT: D 2530 MET cc_start: 0.8418 (ppp) cc_final: 0.7951 (ppp) REVERT: D 2618 MET cc_start: 0.8713 (mpp) cc_final: 0.8080 (mpp) REVERT: D 2874 MET cc_start: -0.5125 (ppp) cc_final: -0.5414 (ptm) REVERT: D 3038 MET cc_start: 0.5924 (ppp) cc_final: 0.4291 (ptm) REVERT: D 3106 MET cc_start: 0.8835 (mmm) cc_final: 0.8512 (mmm) REVERT: D 3435 PHE cc_start: 0.8665 (t80) cc_final: 0.7921 (t80) REVERT: D 3517 MET cc_start: 0.8708 (tpt) cc_final: 0.8495 (tpp) REVERT: D 3518 LEU cc_start: 0.9613 (mt) cc_final: 0.9287 (mt) REVERT: D 3789 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8180 (pp20) REVERT: D 4017 LEU cc_start: 0.9615 (mt) cc_final: 0.9298 (pp) REVERT: D 4107 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.6811 (tp30) REVERT: D 4178 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9176 (tt) REVERT: D 4191 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7990 (mm-30) REVERT: D 4657 CYS cc_start: 0.8974 (m) cc_final: 0.8658 (m) REVERT: D 4880 MET cc_start: 0.9055 (tpp) cc_final: 0.8794 (tpp) REVERT: D 4933 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8565 (mp10) REVERT: D 4942 GLU cc_start: 0.8679 (tt0) cc_final: 0.8416 (mt-10) REVERT: D 4948 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8588 (tm-30) REVERT: D 4965 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8888 (m) REVERT: D 4993 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8467 (ttp) REVERT: D 5012 LYS cc_start: 0.9394 (mptt) cc_final: 0.9145 (mmtm) REVERT: D 5013 MET cc_start: 0.9060 (mtp) cc_final: 0.8680 (mmm) REVERT: D 5035 GLN cc_start: 0.9488 (mt0) cc_final: 0.8989 (mp10) REVERT: E 29 MET cc_start: 0.8968 (mtp) cc_final: 0.8539 (ttp) REVERT: F 29 MET cc_start: 0.8965 (mtp) cc_final: 0.8539 (ttp) REVERT: G 29 MET cc_start: 0.8967 (mtp) cc_final: 0.8538 (ttp) REVERT: H 29 MET cc_start: 0.8966 (mtp) cc_final: 0.8540 (ttp) outliers start: 205 outliers final: 141 residues processed: 1103 average time/residue: 1.1477 time to fit residues: 2298.2424 Evaluate side-chains 1085 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 922 time to evaluate : 12.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1958 LEU Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 4107 GLU Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4635 SER Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4706 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4884 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4927 ILE Chi-restraints excluded: chain A residue 4931 ILE Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4965 SER Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 1958 LEU Chi-restraints excluded: chain B residue 2170 MET Chi-restraints excluded: chain B residue 2256 TYR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 2464 ASP Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 4107 GLU Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4635 SER Chi-restraints excluded: chain B residue 4639 MET Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4706 LEU Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4927 ILE Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 1958 LEU Chi-restraints excluded: chain C residue 2170 MET Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2258 LEU Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 4107 GLU Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4635 SER Chi-restraints excluded: chain C residue 4639 MET Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4706 LEU Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4927 ILE Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4965 SER Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 1958 LEU Chi-restraints excluded: chain D residue 2170 MET Chi-restraints excluded: chain D residue 2256 TYR Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 2464 ASP Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 4107 GLU Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4635 SER Chi-restraints excluded: chain D residue 4639 MET Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4706 LEU Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4927 ILE Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4949 GLN Chi-restraints excluded: chain D residue 4965 SER Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 4993 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 0.7980 chunk 1222 optimal weight: 10.0000 chunk 844 optimal weight: 0.0040 chunk 180 optimal weight: 0.6980 chunk 776 optimal weight: 0.9990 chunk 1092 optimal weight: 20.0000 chunk 1632 optimal weight: 30.0000 chunk 1728 optimal weight: 3.9990 chunk 852 optimal weight: 7.9990 chunk 1547 optimal weight: 10.0000 chunk 465 optimal weight: 0.0570 overall best weight: 0.5112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 GLN A2127 GLN A2444 GLN A2487 GLN A2551 ASN ** A2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4949 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1614 GLN B2127 GLN B2444 GLN B2487 GLN B2551 ASN B4700 GLN B4949 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 ASN C1614 GLN C2127 GLN C2444 GLN C2487 GLN C2551 ASN ** C2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4949 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN D2127 GLN D2444 GLN D2551 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 146364 Z= 0.152 Angle : 0.635 14.807 198272 Z= 0.309 Chirality : 0.041 0.343 21792 Planarity : 0.004 0.057 25772 Dihedral : 5.510 152.013 19720 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 10.31 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.53 (0.06), residues: 17844 helix: 1.31 (0.06), residues: 8652 sheet: -0.57 (0.13), residues: 1612 loop : -0.49 (0.07), residues: 7580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1143 HIS 0.008 0.001 HIS A3771 PHE 0.036 0.001 PHE B3552 TYR 0.023 0.001 TYR B3968 ARG 0.005 0.000 ARG B4189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1009 time to evaluate : 12.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.9371 (mmm) cc_final: 0.8773 (mmm) REVERT: A 846 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7189 (tm) REVERT: A 941 MET cc_start: 0.7008 (tpt) cc_final: 0.6719 (tpt) REVERT: A 1170 MET cc_start: 0.7701 (tpp) cc_final: 0.7319 (tpp) REVERT: A 1230 MET cc_start: 0.8585 (mmm) cc_final: 0.8190 (mmm) REVERT: A 1286 MET cc_start: 0.5771 (tpt) cc_final: 0.5481 (tpt) REVERT: A 1639 LEU cc_start: 0.8939 (tt) cc_final: 0.8232 (tt) REVERT: A 1648 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8426 (pmm) REVERT: A 2198 MET cc_start: 0.9266 (mmt) cc_final: 0.9008 (mpp) REVERT: A 2210 VAL cc_start: 0.9680 (OUTLIER) cc_final: 0.9452 (p) REVERT: A 2211 MET cc_start: 0.9130 (mmm) cc_final: 0.8886 (mmm) REVERT: A 2301 TYR cc_start: 0.8972 (m-10) cc_final: 0.8585 (m-10) REVERT: A 2444 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.9128 (mp10) REVERT: A 2530 MET cc_start: 0.8667 (ppp) cc_final: 0.8217 (ppp) REVERT: A 2618 MET cc_start: 0.8687 (mpp) cc_final: 0.8081 (mpp) REVERT: A 2698 MET cc_start: 0.6840 (ppp) cc_final: 0.6407 (ppp) REVERT: A 3038 MET cc_start: 0.6123 (ppp) cc_final: 0.4634 (ptm) REVERT: A 3081 MET cc_start: 0.0634 (mmt) cc_final: 0.0428 (tpt) REVERT: A 3435 PHE cc_start: 0.8479 (t80) cc_final: 0.8130 (t80) REVERT: A 3517 MET cc_start: 0.8701 (tpp) cc_final: 0.8488 (tpp) REVERT: A 3518 LEU cc_start: 0.9500 (mt) cc_final: 0.9183 (mt) REVERT: A 3814 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8505 (tp-100) REVERT: A 4001 MET cc_start: 0.9068 (mtt) cc_final: 0.8801 (mtt) REVERT: A 4017 LEU cc_start: 0.9550 (mt) cc_final: 0.9246 (pp) REVERT: A 4057 MET cc_start: 0.9288 (ttt) cc_final: 0.8419 (ttt) REVERT: A 4580 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7047 (t80) REVERT: A 4874 MET cc_start: 0.9209 (mmm) cc_final: 0.8800 (mmm) REVERT: A 4933 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8528 (mp10) REVERT: A 4949 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7872 (tp40) REVERT: A 4953 ASP cc_start: 0.9014 (m-30) cc_final: 0.8650 (m-30) REVERT: A 4957 LYS cc_start: 0.9323 (mtmm) cc_final: 0.9117 (mppt) REVERT: A 4993 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8379 (ttp) REVERT: A 5012 LYS cc_start: 0.9380 (mptt) cc_final: 0.9124 (mmtm) REVERT: A 5013 MET cc_start: 0.8902 (mtp) cc_final: 0.8631 (mmm) REVERT: A 5030 LYS cc_start: 0.9550 (ttmt) cc_final: 0.9338 (ttmm) REVERT: B 116 MET cc_start: 0.9365 (mmm) cc_final: 0.8842 (mmm) REVERT: B 127 MET cc_start: 0.8825 (tpp) cc_final: 0.8552 (tmm) REVERT: B 846 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7001 (tm) REVERT: B 877 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7930 (p0) REVERT: B 941 MET cc_start: 0.7114 (tpt) cc_final: 0.6827 (tpt) REVERT: B 1170 MET cc_start: 0.7871 (tpp) cc_final: 0.7476 (tpp) REVERT: B 1286 MET cc_start: 0.5865 (tpt) cc_final: 0.5633 (tpt) REVERT: B 1639 LEU cc_start: 0.9044 (tt) cc_final: 0.8309 (tt) REVERT: B 1648 MET cc_start: 0.8827 (ptp) cc_final: 0.8326 (pmm) REVERT: B 2198 MET cc_start: 0.9205 (mmt) cc_final: 0.8910 (mpp) REVERT: B 2211 MET cc_start: 0.9209 (mmm) cc_final: 0.8984 (mmm) REVERT: B 2301 TYR cc_start: 0.8940 (m-10) cc_final: 0.8565 (m-10) REVERT: B 2444 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9133 (mp10) REVERT: B 2490 MET cc_start: 0.8375 (mmt) cc_final: 0.8130 (mmt) REVERT: B 2502 MET cc_start: 0.9037 (mmp) cc_final: 0.8721 (mmm) REVERT: B 2530 MET cc_start: 0.8609 (ppp) cc_final: 0.8146 (ppp) REVERT: B 2618 MET cc_start: 0.8677 (mpp) cc_final: 0.8073 (mpp) REVERT: B 2874 MET cc_start: -0.5314 (ppp) cc_final: -0.5575 (ptm) REVERT: B 3038 MET cc_start: 0.5853 (ppp) cc_final: 0.4262 (ptm) REVERT: B 3435 PHE cc_start: 0.8624 (t80) cc_final: 0.7745 (t80) REVERT: B 3437 MET cc_start: 0.8982 (mpp) cc_final: 0.8089 (mtt) REVERT: B 3517 MET cc_start: 0.8696 (tpt) cc_final: 0.8432 (tpp) REVERT: B 3518 LEU cc_start: 0.9603 (mt) cc_final: 0.9275 (mt) REVERT: B 3814 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8521 (tp-100) REVERT: B 3999 MET cc_start: 0.8887 (mmm) cc_final: 0.8608 (mmm) REVERT: B 4001 MET cc_start: 0.9060 (mtt) cc_final: 0.8854 (mtt) REVERT: B 4057 MET cc_start: 0.9240 (ttt) cc_final: 0.8423 (ttp) REVERT: B 4580 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.7027 (t80) REVERT: B 4652 LEU cc_start: 0.9572 (tp) cc_final: 0.9354 (tt) REVERT: B 4657 CYS cc_start: 0.8785 (m) cc_final: 0.8564 (m) REVERT: B 4880 MET cc_start: 0.8960 (tpp) cc_final: 0.8730 (tpp) REVERT: B 4949 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7947 (tp40) REVERT: B 4953 ASP cc_start: 0.9019 (m-30) cc_final: 0.8588 (m-30) REVERT: B 4957 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9117 (mppt) REVERT: B 5012 LYS cc_start: 0.9386 (mptt) cc_final: 0.9117 (mmtm) REVERT: B 5013 MET cc_start: 0.8897 (mtp) cc_final: 0.8636 (mmm) REVERT: B 5035 GLN cc_start: 0.9484 (mt0) cc_final: 0.9035 (mp10) REVERT: C 116 MET cc_start: 0.9365 (mmm) cc_final: 0.8843 (mmm) REVERT: C 127 MET cc_start: 0.8823 (tpp) cc_final: 0.8551 (tmm) REVERT: C 226 HIS cc_start: 0.8927 (m-70) cc_final: 0.8714 (m-70) REVERT: C 846 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7004 (tm) REVERT: C 877 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7929 (p0) REVERT: C 941 MET cc_start: 0.7114 (tpt) cc_final: 0.6826 (tpt) REVERT: C 1170 MET cc_start: 0.7868 (tpp) cc_final: 0.7474 (tpp) REVERT: C 1286 MET cc_start: 0.5861 (tpt) cc_final: 0.5628 (tpt) REVERT: C 1639 LEU cc_start: 0.8931 (tt) cc_final: 0.8295 (tt) REVERT: C 1648 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8359 (pmm) REVERT: C 2198 MET cc_start: 0.9204 (mmt) cc_final: 0.8910 (mpp) REVERT: C 2211 MET cc_start: 0.9211 (mmm) cc_final: 0.8985 (mmm) REVERT: C 2301 TYR cc_start: 0.8942 (m-10) cc_final: 0.8565 (m-10) REVERT: C 2444 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.9133 (mp10) REVERT: C 2490 MET cc_start: 0.8375 (mmt) cc_final: 0.8130 (mmt) REVERT: C 2502 MET cc_start: 0.9039 (mmp) cc_final: 0.8722 (mmm) REVERT: C 2530 MET cc_start: 0.8607 (ppp) cc_final: 0.8146 (ppp) REVERT: C 2618 MET cc_start: 0.8679 (mpp) cc_final: 0.8075 (mpp) REVERT: C 2874 MET cc_start: -0.5240 (ppp) cc_final: -0.5512 (ptm) REVERT: C 3038 MET cc_start: 0.5848 (ppp) cc_final: 0.4259 (ptm) REVERT: C 3435 PHE cc_start: 0.8616 (t80) cc_final: 0.7731 (t80) REVERT: C 3437 MET cc_start: 0.8983 (mpp) cc_final: 0.8090 (mtt) REVERT: C 3517 MET cc_start: 0.8697 (tpt) cc_final: 0.8432 (tpp) REVERT: C 3518 LEU cc_start: 0.9602 (mt) cc_final: 0.9274 (mt) REVERT: C 3720 TYR cc_start: 0.8346 (p90) cc_final: 0.8103 (p90) REVERT: C 3789 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8317 (pp20) REVERT: C 3814 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8522 (tp-100) REVERT: C 3999 MET cc_start: 0.8887 (mmm) cc_final: 0.8608 (mmm) REVERT: C 4001 MET cc_start: 0.9060 (mtt) cc_final: 0.8857 (mtt) REVERT: C 4057 MET cc_start: 0.9243 (ttt) cc_final: 0.8423 (ttp) REVERT: C 4580 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.7021 (t80) REVERT: C 4652 LEU cc_start: 0.9573 (tp) cc_final: 0.9353 (tt) REVERT: C 4657 CYS cc_start: 0.8788 (m) cc_final: 0.8569 (m) REVERT: C 4880 MET cc_start: 0.8953 (tpp) cc_final: 0.8732 (tpp) REVERT: C 4933 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8503 (mp10) REVERT: C 4949 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7923 (tp40) REVERT: C 4953 ASP cc_start: 0.9026 (m-30) cc_final: 0.8602 (m-30) REVERT: C 4957 LYS cc_start: 0.9362 (mtmm) cc_final: 0.9119 (mppt) REVERT: C 5012 LYS cc_start: 0.9387 (mptt) cc_final: 0.9118 (mmtm) REVERT: C 5013 MET cc_start: 0.8903 (mtp) cc_final: 0.8638 (mmm) REVERT: C 5032 TYR cc_start: 0.9010 (m-80) cc_final: 0.8635 (m-10) REVERT: C 5035 GLN cc_start: 0.9462 (mt0) cc_final: 0.8996 (mp10) REVERT: D 116 MET cc_start: 0.9366 (mmm) cc_final: 0.8846 (mmm) REVERT: D 127 MET cc_start: 0.8822 (tpp) cc_final: 0.8550 (tmm) REVERT: D 226 HIS cc_start: 0.8932 (m-70) cc_final: 0.8684 (m-70) REVERT: D 846 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7004 (tm) REVERT: D 877 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7928 (p0) REVERT: D 941 MET cc_start: 0.7112 (tpt) cc_final: 0.6824 (tpt) REVERT: D 1170 MET cc_start: 0.7873 (tpp) cc_final: 0.7477 (tpp) REVERT: D 1286 MET cc_start: 0.5862 (tpt) cc_final: 0.5629 (tpt) REVERT: D 1639 LEU cc_start: 0.8933 (tt) cc_final: 0.8298 (tt) REVERT: D 1648 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8359 (pmm) REVERT: D 2198 MET cc_start: 0.9204 (mmt) cc_final: 0.8910 (mpp) REVERT: D 2211 MET cc_start: 0.9211 (mmm) cc_final: 0.8986 (mmm) REVERT: D 2301 TYR cc_start: 0.8927 (m-10) cc_final: 0.8542 (m-10) REVERT: D 2444 GLN cc_start: 0.9357 (OUTLIER) cc_final: 0.9128 (mp10) REVERT: D 2502 MET cc_start: 0.9035 (mmp) cc_final: 0.8717 (mmm) REVERT: D 2530 MET cc_start: 0.8578 (ppp) cc_final: 0.8101 (ppp) REVERT: D 2618 MET cc_start: 0.8677 (mpp) cc_final: 0.8079 (mpp) REVERT: D 2874 MET cc_start: -0.5241 (ppp) cc_final: -0.5513 (ptm) REVERT: D 3038 MET cc_start: 0.5851 (ppp) cc_final: 0.4260 (ptm) REVERT: D 3435 PHE cc_start: 0.8620 (t80) cc_final: 0.7736 (t80) REVERT: D 3437 MET cc_start: 0.8981 (mpp) cc_final: 0.8089 (mtt) REVERT: D 3517 MET cc_start: 0.8699 (tpt) cc_final: 0.8433 (tpp) REVERT: D 3518 LEU cc_start: 0.9603 (mt) cc_final: 0.9275 (mt) REVERT: D 3789 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8316 (pp20) REVERT: D 3814 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8522 (tp-100) REVERT: D 4057 MET cc_start: 0.9240 (ttt) cc_final: 0.8416 (ttp) REVERT: D 4580 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7109 (t80) REVERT: D 4652 LEU cc_start: 0.9572 (tp) cc_final: 0.9352 (tt) REVERT: D 4657 CYS cc_start: 0.8790 (m) cc_final: 0.8572 (m) REVERT: D 4880 MET cc_start: 0.8966 (tpp) cc_final: 0.8740 (tpp) REVERT: D 4933 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: D 4954 MET cc_start: 0.9536 (tpt) cc_final: 0.9176 (mmm) REVERT: D 4957 LYS cc_start: 0.9318 (mtmm) cc_final: 0.9094 (mppt) REVERT: D 5012 LYS cc_start: 0.9385 (mptt) cc_final: 0.9116 (mmtm) REVERT: D 5013 MET cc_start: 0.8905 (mtp) cc_final: 0.8636 (mmm) REVERT: D 5035 GLN cc_start: 0.9484 (mt0) cc_final: 0.9034 (mp10) REVERT: E 29 MET cc_start: 0.8962 (mtp) cc_final: 0.8583 (ttp) REVERT: F 29 MET cc_start: 0.8964 (mtp) cc_final: 0.8584 (ttp) REVERT: G 29 MET cc_start: 0.8963 (mtp) cc_final: 0.8584 (ttp) REVERT: H 29 MET cc_start: 0.8965 (mtp) cc_final: 0.8584 (ttp) outliers start: 160 outliers final: 98 residues processed: 1119 average time/residue: 1.1486 time to fit residues: 2332.3648 Evaluate side-chains 1052 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 928 time to evaluate : 12.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1648 MET Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2444 GLN Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2464 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3638 MET Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 4023 MET Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4556 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 4993 MET Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 877 ASN Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 2170 MET Chi-restraints excluded: chain B residue 2256 TYR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2444 GLN Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 2464 ASP Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3638 MET Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4927 ILE Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 877 ASN Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 1648 MET Chi-restraints excluded: chain C residue 2170 MET Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2258 LEU Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2444 GLN Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3638 MET Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4927 ILE Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 877 ASN Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 1648 MET Chi-restraints excluded: chain D residue 2170 MET Chi-restraints excluded: chain D residue 2256 TYR Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2444 GLN Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 2464 ASP Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3638 MET Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4927 ILE Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4971 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 0.0370 chunk 981 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 1286 optimal weight: 8.9990 chunk 713 optimal weight: 30.0000 chunk 1474 optimal weight: 4.9990 chunk 1194 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 882 optimal weight: 20.0000 chunk 1551 optimal weight: 5.9990 chunk 436 optimal weight: 4.9990 overall best weight: 2.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2127 GLN A2260 ASN ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2441 HIS A2487 GLN ** A2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3608 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2127 GLN ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2441 HIS B2487 GLN ** B2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B3128 ASN ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 ASN ** C1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2127 GLN ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2441 HIS C2487 GLN ** C2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3608 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN ** D1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2127 GLN ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2441 HIS ** D2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 146364 Z= 0.200 Angle : 0.643 14.424 198272 Z= 0.314 Chirality : 0.041 0.365 21792 Planarity : 0.004 0.058 25772 Dihedral : 5.409 154.163 19697 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.21 % Allowed : 11.16 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.60 (0.06), residues: 17844 helix: 1.39 (0.06), residues: 8636 sheet: -0.61 (0.13), residues: 1652 loop : -0.47 (0.07), residues: 7556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D4644 HIS 0.007 0.001 HIS A3771 PHE 0.031 0.001 PHE D3552 TYR 0.037 0.001 TYR A4080 ARG 0.004 0.000 ARG B4189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 943 time to evaluate : 12.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.9348 (mmm) cc_final: 0.8692 (mmm) REVERT: A 846 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7170 (tm) REVERT: A 941 MET cc_start: 0.7052 (tpt) cc_final: 0.6783 (tpt) REVERT: A 1170 MET cc_start: 0.7761 (tpp) cc_final: 0.7420 (tpp) REVERT: A 1230 MET cc_start: 0.8589 (mmm) cc_final: 0.8194 (mmm) REVERT: A 1286 MET cc_start: 0.5818 (tpt) cc_final: 0.5460 (tpt) REVERT: A 1637 MET cc_start: 0.8424 (tpt) cc_final: 0.8170 (tpt) REVERT: A 1648 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8394 (pmm) REVERT: A 1851 MET cc_start: 0.8913 (mmm) cc_final: 0.8669 (mmm) REVERT: A 2203 MET cc_start: 0.9302 (ptp) cc_final: 0.9047 (mpp) REVERT: A 2208 MET cc_start: 0.9217 (ttm) cc_final: 0.8857 (mtp) REVERT: A 2210 VAL cc_start: 0.9692 (OUTLIER) cc_final: 0.9450 (p) REVERT: A 2211 MET cc_start: 0.9228 (mmm) cc_final: 0.8943 (mmm) REVERT: A 2301 TYR cc_start: 0.9013 (m-10) cc_final: 0.8628 (m-10) REVERT: A 2530 MET cc_start: 0.8672 (ppp) cc_final: 0.8203 (ppp) REVERT: A 2618 MET cc_start: 0.8709 (mpp) cc_final: 0.8045 (mpp) REVERT: A 3038 MET cc_start: 0.5917 (ppp) cc_final: 0.4422 (ptm) REVERT: A 3435 PHE cc_start: 0.8605 (t80) cc_final: 0.7975 (t80) REVERT: A 3517 MET cc_start: 0.8762 (tpp) cc_final: 0.8400 (tpp) REVERT: A 3518 LEU cc_start: 0.9509 (mt) cc_final: 0.9205 (mt) REVERT: A 3652 MET cc_start: 0.9287 (pmm) cc_final: 0.8983 (pmm) REVERT: A 3782 MET cc_start: 0.9227 (tpp) cc_final: 0.8549 (tpp) REVERT: A 3999 MET cc_start: 0.8941 (mmm) cc_final: 0.8621 (mmm) REVERT: A 4001 MET cc_start: 0.9059 (mtt) cc_final: 0.8823 (mtt) REVERT: A 4057 MET cc_start: 0.9321 (ttt) cc_final: 0.8390 (ttt) REVERT: A 4580 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7159 (t80) REVERT: A 4874 MET cc_start: 0.9234 (mmm) cc_final: 0.8833 (mmm) REVERT: A 4880 MET cc_start: 0.8956 (tpp) cc_final: 0.8553 (mpp) REVERT: A 4953 ASP cc_start: 0.8954 (m-30) cc_final: 0.8653 (m-30) REVERT: A 4969 ASP cc_start: 0.9217 (m-30) cc_final: 0.8993 (m-30) REVERT: A 5012 LYS cc_start: 0.9368 (mptt) cc_final: 0.9118 (mmtm) REVERT: A 5013 MET cc_start: 0.8910 (mtp) cc_final: 0.8680 (mmm) REVERT: A 5030 LYS cc_start: 0.9550 (ttmt) cc_final: 0.9330 (ttmm) REVERT: B 116 MET cc_start: 0.9368 (mmm) cc_final: 0.8577 (tmm) REVERT: B 127 MET cc_start: 0.8828 (tpp) cc_final: 0.8553 (tmm) REVERT: B 846 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7071 (tm) REVERT: B 941 MET cc_start: 0.7151 (tpt) cc_final: 0.6876 (tpt) REVERT: B 1170 MET cc_start: 0.7859 (tpp) cc_final: 0.7524 (tpp) REVERT: B 1286 MET cc_start: 0.5887 (tpt) cc_final: 0.5578 (tpt) REVERT: B 1639 LEU cc_start: 0.9111 (tt) cc_final: 0.8307 (tt) REVERT: B 1648 MET cc_start: 0.8820 (ptp) cc_final: 0.8369 (pmm) REVERT: B 1851 MET cc_start: 0.8918 (mmm) cc_final: 0.8562 (mmm) REVERT: B 2203 MET cc_start: 0.9302 (ptp) cc_final: 0.9048 (mpp) REVERT: B 2208 MET cc_start: 0.9084 (ttm) cc_final: 0.8807 (mtp) REVERT: B 2301 TYR cc_start: 0.8961 (m-10) cc_final: 0.8579 (m-10) REVERT: B 2490 MET cc_start: 0.8318 (mmt) cc_final: 0.8090 (mmt) REVERT: B 2530 MET cc_start: 0.8691 (ppp) cc_final: 0.8213 (ppp) REVERT: B 2618 MET cc_start: 0.8700 (mpp) cc_final: 0.8078 (mpp) REVERT: B 2874 MET cc_start: -0.5290 (ppp) cc_final: -0.5554 (ptm) REVERT: B 3038 MET cc_start: 0.5984 (ppp) cc_final: 0.4475 (ptm) REVERT: B 3435 PHE cc_start: 0.8580 (t80) cc_final: 0.7846 (t80) REVERT: B 3517 MET cc_start: 0.8736 (tpt) cc_final: 0.8479 (tpp) REVERT: B 3518 LEU cc_start: 0.9613 (mt) cc_final: 0.9288 (mt) REVERT: B 3652 MET cc_start: 0.9282 (pmm) cc_final: 0.9024 (pmm) REVERT: B 3673 MET cc_start: 0.9408 (mmm) cc_final: 0.9047 (tpp) REVERT: B 3782 MET cc_start: 0.9212 (tpp) cc_final: 0.8562 (tpp) REVERT: B 4580 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7096 (t80) REVERT: B 4657 CYS cc_start: 0.8932 (m) cc_final: 0.8599 (m) REVERT: B 4880 MET cc_start: 0.9054 (tpp) cc_final: 0.8811 (tpp) REVERT: B 4933 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: B 4948 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8577 (tm-30) REVERT: B 4957 LYS cc_start: 0.9409 (mtmm) cc_final: 0.9175 (mppt) REVERT: B 4965 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8762 (m) REVERT: B 5012 LYS cc_start: 0.9367 (mptt) cc_final: 0.9106 (mmtm) REVERT: B 5013 MET cc_start: 0.8921 (mtp) cc_final: 0.8680 (mmm) REVERT: B 5035 GLN cc_start: 0.9470 (mt0) cc_final: 0.9010 (mp10) REVERT: C 116 MET cc_start: 0.9367 (mmm) cc_final: 0.8578 (tmm) REVERT: C 127 MET cc_start: 0.8828 (tpp) cc_final: 0.8551 (tmm) REVERT: C 226 HIS cc_start: 0.8931 (m-70) cc_final: 0.8730 (m-70) REVERT: C 846 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7074 (tm) REVERT: C 941 MET cc_start: 0.7149 (tpt) cc_final: 0.6875 (tpt) REVERT: C 1170 MET cc_start: 0.7856 (tpp) cc_final: 0.7521 (tpp) REVERT: C 1286 MET cc_start: 0.5884 (tpt) cc_final: 0.5577 (tpt) REVERT: C 1648 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8325 (pmm) REVERT: C 1851 MET cc_start: 0.8919 (mmm) cc_final: 0.8562 (mmm) REVERT: C 2203 MET cc_start: 0.9302 (ptp) cc_final: 0.9049 (mpp) REVERT: C 2208 MET cc_start: 0.9087 (ttm) cc_final: 0.8809 (mtp) REVERT: C 2301 TYR cc_start: 0.8961 (m-10) cc_final: 0.8579 (m-10) REVERT: C 2490 MET cc_start: 0.8320 (mmt) cc_final: 0.8091 (mmt) REVERT: C 2530 MET cc_start: 0.8685 (ppp) cc_final: 0.8211 (ppp) REVERT: C 2618 MET cc_start: 0.8702 (mpp) cc_final: 0.8081 (mpp) REVERT: C 2874 MET cc_start: -0.5308 (ppp) cc_final: -0.5562 (ptm) REVERT: C 3038 MET cc_start: 0.5981 (ppp) cc_final: 0.4469 (ptm) REVERT: C 3435 PHE cc_start: 0.8580 (t80) cc_final: 0.7848 (t80) REVERT: C 3517 MET cc_start: 0.8736 (tpt) cc_final: 0.8480 (tpp) REVERT: C 3518 LEU cc_start: 0.9612 (mt) cc_final: 0.9288 (mt) REVERT: C 3652 MET cc_start: 0.9283 (pmm) cc_final: 0.8965 (pmm) REVERT: C 3673 MET cc_start: 0.9420 (mmm) cc_final: 0.9070 (tpp) REVERT: C 3720 TYR cc_start: 0.8351 (p90) cc_final: 0.8068 (p90) REVERT: C 3782 MET cc_start: 0.9211 (tpp) cc_final: 0.8582 (tpp) REVERT: C 4191 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7990 (mm-30) REVERT: C 4580 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7096 (t80) REVERT: C 4657 CYS cc_start: 0.8933 (m) cc_final: 0.8599 (m) REVERT: C 4880 MET cc_start: 0.9046 (tpp) cc_final: 0.8806 (tpp) REVERT: C 4933 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8560 (mp10) REVERT: C 4948 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8589 (tm-30) REVERT: C 4957 LYS cc_start: 0.9412 (mtmm) cc_final: 0.9180 (mppt) REVERT: C 4993 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8512 (ttp) REVERT: C 5012 LYS cc_start: 0.9368 (mptt) cc_final: 0.9107 (mmtm) REVERT: C 5013 MET cc_start: 0.8928 (mtp) cc_final: 0.8685 (mmm) REVERT: C 5032 TYR cc_start: 0.9073 (m-80) cc_final: 0.8812 (m-10) REVERT: C 5035 GLN cc_start: 0.9444 (mt0) cc_final: 0.9015 (mp10) REVERT: D 116 MET cc_start: 0.9368 (mmm) cc_final: 0.8577 (tmm) REVERT: D 127 MET cc_start: 0.8826 (tpp) cc_final: 0.8550 (tmm) REVERT: D 846 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7074 (tm) REVERT: D 941 MET cc_start: 0.7045 (tpt) cc_final: 0.6759 (tpt) REVERT: D 1170 MET cc_start: 0.7856 (tpp) cc_final: 0.7523 (tpp) REVERT: D 1286 MET cc_start: 0.5886 (tpt) cc_final: 0.5575 (tpt) REVERT: D 1648 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8325 (pmm) REVERT: D 1851 MET cc_start: 0.8922 (mmm) cc_final: 0.8564 (mmm) REVERT: D 2203 MET cc_start: 0.9302 (ptp) cc_final: 0.9049 (mpp) REVERT: D 2208 MET cc_start: 0.9086 (ttm) cc_final: 0.8808 (mtp) REVERT: D 2301 TYR cc_start: 0.8962 (m-10) cc_final: 0.8579 (m-10) REVERT: D 2490 MET cc_start: 0.7765 (mmt) cc_final: 0.7333 (mmt) REVERT: D 2618 MET cc_start: 0.8698 (mpp) cc_final: 0.8084 (mpp) REVERT: D 2874 MET cc_start: -0.5221 (ppp) cc_final: -0.5480 (ptm) REVERT: D 3038 MET cc_start: 0.5982 (ppp) cc_final: 0.4470 (ptm) REVERT: D 3435 PHE cc_start: 0.8585 (t80) cc_final: 0.7853 (t80) REVERT: D 3517 MET cc_start: 0.8740 (tpt) cc_final: 0.8482 (tpp) REVERT: D 3518 LEU cc_start: 0.9612 (mt) cc_final: 0.9288 (mt) REVERT: D 3652 MET cc_start: 0.9282 (pmm) cc_final: 0.8965 (pmm) REVERT: D 3673 MET cc_start: 0.9419 (mmm) cc_final: 0.9069 (tpp) REVERT: D 3782 MET cc_start: 0.9201 (tpp) cc_final: 0.8568 (tpp) REVERT: D 4580 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7032 (t80) REVERT: D 4657 CYS cc_start: 0.8935 (m) cc_final: 0.8601 (m) REVERT: D 4880 MET cc_start: 0.9058 (tpp) cc_final: 0.8808 (tpp) REVERT: D 4933 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8564 (mp10) REVERT: D 4954 MET cc_start: 0.9531 (tpt) cc_final: 0.9154 (mmm) REVERT: D 4957 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9141 (mppt) REVERT: D 5012 LYS cc_start: 0.9366 (mptt) cc_final: 0.9105 (mmtm) REVERT: D 5013 MET cc_start: 0.8928 (mtp) cc_final: 0.8684 (mmm) REVERT: D 5035 GLN cc_start: 0.9472 (mt0) cc_final: 0.9011 (mp10) REVERT: E 29 MET cc_start: 0.8978 (mtp) cc_final: 0.8515 (ttp) REVERT: F 29 MET cc_start: 0.8978 (mtp) cc_final: 0.8516 (ttp) REVERT: G 29 MET cc_start: 0.8977 (mtp) cc_final: 0.8515 (ttp) REVERT: H 29 MET cc_start: 0.8978 (mtp) cc_final: 0.8516 (ttp) outliers start: 176 outliers final: 121 residues processed: 1060 average time/residue: 1.1684 time to fit residues: 2250.0165 Evaluate side-chains 1047 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 909 time to evaluate : 12.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1648 MET Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2464 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3638 MET Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 4023 MET Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4556 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4884 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 1636 MET Chi-restraints excluded: chain B residue 2170 MET Chi-restraints excluded: chain B residue 2256 TYR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 2464 ASP Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3638 MET Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 4146 LEU Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4639 MET Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4965 SER Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 1636 MET Chi-restraints excluded: chain C residue 1648 MET Chi-restraints excluded: chain C residue 2170 MET Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2258 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 2464 ASP Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3638 MET Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4639 MET Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 1636 MET Chi-restraints excluded: chain D residue 1648 MET Chi-restraints excluded: chain D residue 2170 MET Chi-restraints excluded: chain D residue 2256 TYR Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 2464 ASP Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3638 MET Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 4146 LEU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4639 MET Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4992 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 0.0170 chunk 1556 optimal weight: 4.9990 chunk 341 optimal weight: 7.9990 chunk 1014 optimal weight: 10.0000 chunk 426 optimal weight: 4.9990 chunk 1729 optimal weight: 0.7980 chunk 1436 optimal weight: 30.0000 chunk 800 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 572 optimal weight: 1.9990 chunk 908 optimal weight: 8.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2127 GLN ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2444 GLN A2487 GLN ** A2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2127 GLN ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2444 GLN ** B2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4216 GLN B4949 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2127 GLN ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2444 GLN ** C2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4949 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2127 GLN ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2444 GLN ** D2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4216 GLN E 87 HIS F 87 HIS G 87 HIS H 87 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 146364 Z= 0.177 Angle : 0.643 14.903 198272 Z= 0.312 Chirality : 0.042 0.362 21792 Planarity : 0.004 0.058 25772 Dihedral : 5.311 152.773 19679 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.12 % Allowed : 11.94 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.61 (0.06), residues: 17844 helix: 1.41 (0.06), residues: 8660 sheet: -0.62 (0.13), residues: 1652 loop : -0.48 (0.07), residues: 7532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D4644 HIS 0.007 0.001 HIS A3771 PHE 0.029 0.001 PHE C2973 TYR 0.029 0.001 TYR A4080 ARG 0.012 0.000 ARG D2575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 929 time to evaluate : 12.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 MET cc_start: 0.9334 (mmm) cc_final: 0.8698 (mmm) REVERT: A 846 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7121 (tm) REVERT: A 941 MET cc_start: 0.7088 (tpt) cc_final: 0.6814 (tpt) REVERT: A 1170 MET cc_start: 0.7796 (tpp) cc_final: 0.7446 (tpp) REVERT: A 1230 MET cc_start: 0.8587 (mmm) cc_final: 0.8198 (mmm) REVERT: A 1286 MET cc_start: 0.5877 (tpt) cc_final: 0.5569 (tpt) REVERT: A 1637 MET cc_start: 0.8470 (tpt) cc_final: 0.8115 (tpt) REVERT: A 1639 LEU cc_start: 0.8982 (tt) cc_final: 0.8241 (tt) REVERT: A 1648 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8520 (pmm) REVERT: A 1851 MET cc_start: 0.8913 (mmm) cc_final: 0.8613 (mmm) REVERT: A 2198 MET cc_start: 0.9291 (mmt) cc_final: 0.8994 (mpp) REVERT: A 2210 VAL cc_start: 0.9685 (OUTLIER) cc_final: 0.9448 (p) REVERT: A 2211 MET cc_start: 0.9230 (mmm) cc_final: 0.8949 (mmm) REVERT: A 2301 TYR cc_start: 0.9000 (m-10) cc_final: 0.8766 (m-10) REVERT: A 2530 MET cc_start: 0.8709 (ppp) cc_final: 0.8168 (ppp) REVERT: A 2618 MET cc_start: 0.8698 (mpp) cc_final: 0.8029 (mpp) REVERT: A 3038 MET cc_start: 0.5926 (ppp) cc_final: 0.4484 (ptm) REVERT: A 3435 PHE cc_start: 0.8554 (t80) cc_final: 0.7900 (t80) REVERT: A 3517 MET cc_start: 0.8755 (tpp) cc_final: 0.8415 (tpp) REVERT: A 3518 LEU cc_start: 0.9504 (mt) cc_final: 0.9203 (mt) REVERT: A 3782 MET cc_start: 0.9234 (tpp) cc_final: 0.8508 (tpp) REVERT: A 3793 MET cc_start: 0.8841 (mmm) cc_final: 0.8608 (tpp) REVERT: A 3999 MET cc_start: 0.9028 (mmm) cc_final: 0.8662 (mmm) REVERT: A 4580 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.7231 (t80) REVERT: A 4874 MET cc_start: 0.9214 (mmm) cc_final: 0.8835 (mmm) REVERT: A 4880 MET cc_start: 0.9032 (tpp) cc_final: 0.8608 (mpp) REVERT: A 4953 ASP cc_start: 0.8707 (m-30) cc_final: 0.8456 (m-30) REVERT: A 4969 ASP cc_start: 0.9232 (m-30) cc_final: 0.8988 (m-30) REVERT: A 5012 LYS cc_start: 0.9378 (mptt) cc_final: 0.9103 (mmtm) REVERT: A 5013 MET cc_start: 0.8869 (mtp) cc_final: 0.8664 (mmm) REVERT: A 5030 LYS cc_start: 0.9570 (ttmt) cc_final: 0.9357 (ttmm) REVERT: B 116 MET cc_start: 0.9364 (mmm) cc_final: 0.8662 (mmm) REVERT: B 127 MET cc_start: 0.8793 (tpp) cc_final: 0.8514 (tmm) REVERT: B 227 MET cc_start: 0.8443 (pmm) cc_final: 0.8238 (pmm) REVERT: B 846 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7054 (tm) REVERT: B 941 MET cc_start: 0.7107 (tpt) cc_final: 0.6823 (tpt) REVERT: B 1170 MET cc_start: 0.7879 (tpp) cc_final: 0.7539 (tpp) REVERT: B 1230 MET cc_start: 0.8704 (mmm) cc_final: 0.8360 (mmm) REVERT: B 1286 MET cc_start: 0.5994 (tpt) cc_final: 0.5723 (tpt) REVERT: B 1648 MET cc_start: 0.8723 (ptp) cc_final: 0.8317 (pmm) REVERT: B 1851 MET cc_start: 0.8935 (mmm) cc_final: 0.8651 (mmm) REVERT: B 2198 MET cc_start: 0.9297 (mmt) cc_final: 0.8996 (mpp) REVERT: B 2208 MET cc_start: 0.9111 (ttm) cc_final: 0.8776 (mtp) REVERT: B 2301 TYR cc_start: 0.9006 (m-10) cc_final: 0.8608 (m-10) REVERT: B 2490 MET cc_start: 0.8319 (mmp) cc_final: 0.8106 (mmt) REVERT: B 2530 MET cc_start: 0.8724 (ppp) cc_final: 0.8362 (ppp) REVERT: B 2618 MET cc_start: 0.8685 (mpp) cc_final: 0.8058 (mpp) REVERT: B 3038 MET cc_start: 0.5995 (ppp) cc_final: 0.4532 (ptm) REVERT: B 3435 PHE cc_start: 0.8601 (t80) cc_final: 0.8076 (t80) REVERT: B 3518 LEU cc_start: 0.9614 (mt) cc_final: 0.9302 (mt) REVERT: B 3673 MET cc_start: 0.9408 (mmm) cc_final: 0.9045 (tpp) REVERT: B 3782 MET cc_start: 0.9231 (tpp) cc_final: 0.8548 (tpp) REVERT: B 3793 MET cc_start: 0.8861 (mmm) cc_final: 0.8648 (tpp) REVERT: B 4072 VAL cc_start: 0.3886 (m) cc_final: 0.3685 (m) REVERT: B 4191 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8023 (mm-30) REVERT: B 4580 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7218 (t80) REVERT: B 4657 CYS cc_start: 0.8822 (m) cc_final: 0.8590 (m) REVERT: B 4880 MET cc_start: 0.9030 (tpp) cc_final: 0.8782 (tpp) REVERT: B 4933 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8361 (mp10) REVERT: B 4953 ASP cc_start: 0.8900 (m-30) cc_final: 0.8665 (m-30) REVERT: B 4957 LYS cc_start: 0.9402 (mtmm) cc_final: 0.9146 (mppt) REVERT: B 5012 LYS cc_start: 0.9388 (mptt) cc_final: 0.9107 (mmtm) REVERT: B 5013 MET cc_start: 0.8876 (mtp) cc_final: 0.8655 (mmm) REVERT: B 5035 GLN cc_start: 0.9492 (mt0) cc_final: 0.9049 (mp10) REVERT: C 116 MET cc_start: 0.9363 (mmm) cc_final: 0.8662 (mmm) REVERT: C 127 MET cc_start: 0.8793 (tpp) cc_final: 0.8514 (tmm) REVERT: C 846 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7054 (tm) REVERT: C 941 MET cc_start: 0.7107 (tpt) cc_final: 0.6824 (tpt) REVERT: C 1170 MET cc_start: 0.7882 (tpp) cc_final: 0.7539 (tpp) REVERT: C 1230 MET cc_start: 0.8703 (mmm) cc_final: 0.8364 (mmm) REVERT: C 1286 MET cc_start: 0.5986 (tpt) cc_final: 0.5718 (tpt) REVERT: C 1648 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8484 (pmm) REVERT: C 1851 MET cc_start: 0.8913 (mmm) cc_final: 0.8623 (mmm) REVERT: C 2198 MET cc_start: 0.9296 (mmt) cc_final: 0.8995 (mpp) REVERT: C 2208 MET cc_start: 0.9113 (ttm) cc_final: 0.8817 (mtp) REVERT: C 2301 TYR cc_start: 0.9006 (m-10) cc_final: 0.8607 (m-10) REVERT: C 2490 MET cc_start: 0.8320 (mmp) cc_final: 0.8107 (mmt) REVERT: C 2530 MET cc_start: 0.8719 (ppp) cc_final: 0.8174 (ppp) REVERT: C 2618 MET cc_start: 0.8689 (mpp) cc_final: 0.8063 (mpp) REVERT: C 3038 MET cc_start: 0.5989 (ppp) cc_final: 0.4527 (ptm) REVERT: C 3435 PHE cc_start: 0.8601 (t80) cc_final: 0.8076 (t80) REVERT: C 3518 LEU cc_start: 0.9613 (mt) cc_final: 0.9302 (mt) REVERT: C 3673 MET cc_start: 0.9408 (mmm) cc_final: 0.9045 (tpp) REVERT: C 3782 MET cc_start: 0.9232 (tpp) cc_final: 0.8503 (tpp) REVERT: C 3793 MET cc_start: 0.8864 (mmm) cc_final: 0.8649 (tpp) REVERT: C 4072 VAL cc_start: 0.3882 (m) cc_final: 0.3678 (m) REVERT: C 4191 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8030 (mm-30) REVERT: C 4578 LEU cc_start: 0.9161 (mt) cc_final: 0.8361 (tp) REVERT: C 4580 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7220 (t80) REVERT: C 4657 CYS cc_start: 0.8825 (m) cc_final: 0.8592 (m) REVERT: C 4880 MET cc_start: 0.9023 (tpp) cc_final: 0.8780 (tpp) REVERT: C 4933 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: C 4953 ASP cc_start: 0.8905 (m-30) cc_final: 0.8678 (m-30) REVERT: C 4957 LYS cc_start: 0.9396 (mtmm) cc_final: 0.9160 (mppt) REVERT: C 4993 MET cc_start: 0.8719 (mtp) cc_final: 0.8501 (ttp) REVERT: C 5012 LYS cc_start: 0.9382 (mptt) cc_final: 0.9098 (mmtm) REVERT: C 5013 MET cc_start: 0.8880 (mtp) cc_final: 0.8659 (mmm) REVERT: C 5032 TYR cc_start: 0.9046 (m-80) cc_final: 0.8664 (m-10) REVERT: C 5035 GLN cc_start: 0.9430 (mt0) cc_final: 0.9002 (mp10) REVERT: D 116 MET cc_start: 0.9365 (mmm) cc_final: 0.8663 (mmm) REVERT: D 127 MET cc_start: 0.8791 (tpp) cc_final: 0.8512 (tmm) REVERT: D 846 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7057 (tm) REVERT: D 941 MET cc_start: 0.7068 (tpt) cc_final: 0.6794 (tpt) REVERT: D 1170 MET cc_start: 0.7878 (tpp) cc_final: 0.7537 (tpp) REVERT: D 1230 MET cc_start: 0.8704 (mmm) cc_final: 0.8364 (mmm) REVERT: D 1286 MET cc_start: 0.5992 (tpt) cc_final: 0.5718 (tpt) REVERT: D 1648 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8484 (pmm) REVERT: D 1851 MET cc_start: 0.8936 (mmm) cc_final: 0.8653 (mmm) REVERT: D 2198 MET cc_start: 0.9296 (mmt) cc_final: 0.8996 (mpp) REVERT: D 2208 MET cc_start: 0.9155 (ttm) cc_final: 0.8925 (mtp) REVERT: D 2301 TYR cc_start: 0.9007 (m-10) cc_final: 0.8607 (m-10) REVERT: D 2530 MET cc_start: 0.8530 (ppp) cc_final: 0.7975 (ppp) REVERT: D 2618 MET cc_start: 0.8688 (mpp) cc_final: 0.8067 (mpp) REVERT: D 3038 MET cc_start: 0.5997 (ppp) cc_final: 0.4533 (ptm) REVERT: D 3435 PHE cc_start: 0.8603 (t80) cc_final: 0.8077 (t80) REVERT: D 3518 LEU cc_start: 0.9613 (mt) cc_final: 0.9301 (mt) REVERT: D 3673 MET cc_start: 0.9407 (mmm) cc_final: 0.9045 (tpp) REVERT: D 3782 MET cc_start: 0.9217 (tpp) cc_final: 0.8518 (tpp) REVERT: D 3793 MET cc_start: 0.8858 (mmm) cc_final: 0.8644 (tpp) REVERT: D 4191 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8021 (mm-30) REVERT: D 4580 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7172 (t80) REVERT: D 4657 CYS cc_start: 0.8824 (m) cc_final: 0.8591 (m) REVERT: D 4880 MET cc_start: 0.9030 (tpp) cc_final: 0.8701 (tpp) REVERT: D 4933 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: D 4954 MET cc_start: 0.9536 (tpt) cc_final: 0.9177 (mmm) REVERT: D 4957 LYS cc_start: 0.9344 (mtmm) cc_final: 0.9090 (mppt) REVERT: D 5012 LYS cc_start: 0.9381 (mptt) cc_final: 0.9097 (mmtm) REVERT: D 5013 MET cc_start: 0.8880 (mtp) cc_final: 0.8659 (mmm) REVERT: D 5035 GLN cc_start: 0.9492 (mt0) cc_final: 0.9049 (mp10) REVERT: E 29 MET cc_start: 0.8970 (mtp) cc_final: 0.8507 (ttp) REVERT: F 29 MET cc_start: 0.8971 (mtp) cc_final: 0.8508 (ttp) REVERT: G 29 MET cc_start: 0.8971 (mtp) cc_final: 0.8508 (ttp) REVERT: H 29 MET cc_start: 0.8971 (mtp) cc_final: 0.8508 (ttp) outliers start: 159 outliers final: 127 residues processed: 1037 average time/residue: 1.1801 time to fit residues: 2223.2421 Evaluate side-chains 1063 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 921 time to evaluate : 12.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1636 MET Chi-restraints excluded: chain A residue 1648 MET Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2256 TYR Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2464 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3638 MET Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 3701 LEU Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4556 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4884 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1120 LEU Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 1636 MET Chi-restraints excluded: chain B residue 2256 TYR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 2464 ASP Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3638 MET Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 3701 LEU Chi-restraints excluded: chain B residue 4146 LEU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4639 MET Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4736 ARG Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1120 LEU Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 1636 MET Chi-restraints excluded: chain C residue 1648 MET Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2258 LEU Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 2464 ASP Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3638 MET Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 3701 LEU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4639 MET Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4736 ARG Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1120 LEU Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 1636 MET Chi-restraints excluded: chain D residue 1648 MET Chi-restraints excluded: chain D residue 2256 TYR Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 2464 ASP Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3638 MET Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 3701 LEU Chi-restraints excluded: chain D residue 4146 LEU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4639 MET Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 985 optimal weight: 20.0000 chunk 1263 optimal weight: 2.9990 chunk 978 optimal weight: 10.0000 chunk 1456 optimal weight: 9.9990 chunk 966 optimal weight: 50.0000 chunk 1723 optimal weight: 7.9990 chunk 1078 optimal weight: 9.9990 chunk 1050 optimal weight: 9.9990 chunk 795 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1231 GLN B ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 GLN ** A1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2127 GLN ** A2204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2247 GLN ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2487 GLN A2551 ASN ** A2881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2991 HIS ** A3357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4120 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1231 GLN B ** B1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1614 GLN ** B1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2127 GLN ** B2204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2247 GLN ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2551 ASN B2991 HIS ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4120 ASN B4216 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 HIS C1231 GLN B ** C1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1614 GLN ** C1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2127 GLN ** C2204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2247 GLN ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2551 ASN ** C2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C2991 HIS ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4120 ASN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 HIS D1231 GLN B ** D1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2127 GLN ** D2204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2247 GLN ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D2991 HIS ** D3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3608 GLN D4216 GLN E 20 GLN F 20 GLN G 20 GLN H 20 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 146364 Z= 0.430 Angle : 0.794 15.342 198272 Z= 0.399 Chirality : 0.045 0.349 21792 Planarity : 0.005 0.084 25772 Dihedral : 5.677 157.195 19676 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.41 % Rotamer: Outliers : 1.31 % Allowed : 12.53 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.19 (0.06), residues: 17844 helix: 1.00 (0.06), residues: 8708 sheet: -0.82 (0.13), residues: 1576 loop : -0.60 (0.07), residues: 7560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1005 HIS 0.012 0.002 HIS D4983 PHE 0.034 0.002 PHE B3899 TYR 0.029 0.002 TYR A4080 ARG 0.013 0.001 ARG B2575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 899 time to evaluate : 12.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 116 MET cc_start: 0.9254 (mmm) cc_final: 0.8757 (mmm) REVERT: A 846 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7354 (tm) REVERT: A 941 MET cc_start: 0.7420 (tpt) cc_final: 0.7197 (tpt) REVERT: A 1170 MET cc_start: 0.7931 (tpp) cc_final: 0.7698 (tpp) REVERT: A 1286 MET cc_start: 0.5994 (tpt) cc_final: 0.5671 (tpt) REVERT: A 1494 MET cc_start: 0.7893 (tpp) cc_final: 0.7490 (mmt) REVERT: A 1851 MET cc_start: 0.9007 (mmm) cc_final: 0.8746 (mmm) REVERT: A 2208 MET cc_start: 0.9197 (ttm) cc_final: 0.8733 (mtp) REVERT: A 2210 VAL cc_start: 0.9728 (OUTLIER) cc_final: 0.9469 (p) REVERT: A 2211 MET cc_start: 0.9348 (mmm) cc_final: 0.9110 (mmm) REVERT: A 2530 MET cc_start: 0.8802 (ppp) cc_final: 0.8339 (ppp) REVERT: A 2618 MET cc_start: 0.8704 (mpp) cc_final: 0.7992 (mpp) REVERT: A 3038 MET cc_start: 0.6517 (ppp) cc_final: 0.5259 (ptm) REVERT: A 3435 PHE cc_start: 0.8671 (t80) cc_final: 0.8019 (t80) REVERT: A 3517 MET cc_start: 0.8822 (tpp) cc_final: 0.8568 (tpp) REVERT: A 3518 LEU cc_start: 0.9477 (mt) cc_final: 0.9159 (mt) REVERT: A 3723 MET cc_start: 0.9193 (mmp) cc_final: 0.8884 (mmp) REVERT: A 4580 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.6894 (t80) REVERT: A 4657 CYS cc_start: 0.8782 (m) cc_final: 0.8534 (m) REVERT: A 4874 MET cc_start: 0.9102 (mmm) cc_final: 0.8772 (mmm) REVERT: A 4880 MET cc_start: 0.9079 (tpp) cc_final: 0.8730 (mpp) REVERT: A 4954 MET cc_start: 0.9417 (mmm) cc_final: 0.9200 (mmm) REVERT: A 4965 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8470 (m) REVERT: A 5012 LYS cc_start: 0.9429 (mptt) cc_final: 0.9139 (mmtm) REVERT: A 5013 MET cc_start: 0.9088 (mtp) cc_final: 0.8708 (mmm) REVERT: A 5030 LYS cc_start: 0.9630 (ttmt) cc_final: 0.9393 (ttmm) REVERT: A 5035 GLN cc_start: 0.9463 (mt0) cc_final: 0.8992 (mp10) REVERT: B 127 MET cc_start: 0.8736 (tpp) cc_final: 0.8449 (tmm) REVERT: B 228 ASP cc_start: 0.9264 (m-30) cc_final: 0.9026 (m-30) REVERT: B 846 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7362 (tm) REVERT: B 924 MET cc_start: 0.6660 (ptp) cc_final: 0.6455 (tmm) REVERT: B 941 MET cc_start: 0.7285 (tpt) cc_final: 0.7017 (tpt) REVERT: B 1170 MET cc_start: 0.7980 (tpp) cc_final: 0.7756 (tpp) REVERT: B 1286 MET cc_start: 0.6002 (tpt) cc_final: 0.5642 (tpt) REVERT: B 1851 MET cc_start: 0.9000 (mmm) cc_final: 0.8734 (mmm) REVERT: B 2530 MET cc_start: 0.8814 (ppp) cc_final: 0.8320 (ppp) REVERT: B 2618 MET cc_start: 0.8733 (mpp) cc_final: 0.8017 (mpp) REVERT: B 2874 MET cc_start: -0.5600 (ptm) cc_final: -0.5818 (ptm) REVERT: B 3038 MET cc_start: 0.6565 (ppp) cc_final: 0.5341 (ptm) REVERT: B 3435 PHE cc_start: 0.8785 (t80) cc_final: 0.8280 (t80) REVERT: B 3518 LEU cc_start: 0.9550 (mt) cc_final: 0.9195 (mt) REVERT: B 4000 MET cc_start: 0.9270 (ptp) cc_final: 0.9010 (ptp) REVERT: B 4023 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8977 (tmm) REVERT: B 4097 MET cc_start: -0.3396 (mtp) cc_final: -0.3751 (mtp) REVERT: B 4122 MET cc_start: 0.1819 (tpp) cc_final: 0.1338 (tpt) REVERT: B 4227 GLU cc_start: 0.8681 (pm20) cc_final: 0.7908 (pp20) REVERT: B 4580 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.6979 (t80) REVERT: B 4657 CYS cc_start: 0.8937 (m) cc_final: 0.8635 (m) REVERT: B 4880 MET cc_start: 0.9094 (tpp) cc_final: 0.8651 (tpp) REVERT: B 4953 ASP cc_start: 0.9124 (m-30) cc_final: 0.8683 (m-30) REVERT: B 4965 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8575 (m) REVERT: B 5012 LYS cc_start: 0.9418 (mptt) cc_final: 0.9124 (mmtm) REVERT: B 5013 MET cc_start: 0.9094 (mtp) cc_final: 0.8715 (mmm) REVERT: B 5035 GLN cc_start: 0.9515 (mt0) cc_final: 0.9077 (mp10) REVERT: C 116 MET cc_start: 0.9267 (mmm) cc_final: 0.8583 (mmm) REVERT: C 127 MET cc_start: 0.8736 (tpp) cc_final: 0.8448 (tmm) REVERT: C 228 ASP cc_start: 0.9252 (m-30) cc_final: 0.9035 (m-30) REVERT: C 846 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7367 (tm) REVERT: C 924 MET cc_start: 0.6661 (ptp) cc_final: 0.6457 (tmm) REVERT: C 941 MET cc_start: 0.7392 (tpt) cc_final: 0.7139 (tpt) REVERT: C 1170 MET cc_start: 0.7982 (tpp) cc_final: 0.7755 (tpp) REVERT: C 1286 MET cc_start: 0.5990 (tpt) cc_final: 0.5638 (tpt) REVERT: C 1851 MET cc_start: 0.9004 (mmm) cc_final: 0.8752 (mmm) REVERT: C 2530 MET cc_start: 0.8812 (ppp) cc_final: 0.8356 (ppp) REVERT: C 2618 MET cc_start: 0.8705 (mpp) cc_final: 0.7999 (mpp) REVERT: C 2874 MET cc_start: -0.5625 (ptm) cc_final: -0.5830 (ptm) REVERT: C 3038 MET cc_start: 0.6560 (ppp) cc_final: 0.5336 (ptm) REVERT: C 3435 PHE cc_start: 0.8784 (t80) cc_final: 0.8280 (t80) REVERT: C 3518 LEU cc_start: 0.9549 (mt) cc_final: 0.9194 (mt) REVERT: C 4000 MET cc_start: 0.9267 (ptp) cc_final: 0.9007 (ptp) REVERT: C 4023 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8976 (tmm) REVERT: C 4097 MET cc_start: -0.3408 (mtp) cc_final: -0.3762 (mtp) REVERT: C 4122 MET cc_start: 0.1813 (tpp) cc_final: 0.1337 (tpt) REVERT: C 4580 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.6900 (t80) REVERT: C 4880 MET cc_start: 0.9096 (tpp) cc_final: 0.8635 (tpp) REVERT: C 4953 ASP cc_start: 0.9156 (m-30) cc_final: 0.8836 (m-30) REVERT: C 4965 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8555 (m) REVERT: C 4993 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8605 (ttp) REVERT: C 5012 LYS cc_start: 0.9417 (mptt) cc_final: 0.9123 (mmtm) REVERT: C 5013 MET cc_start: 0.9096 (mtp) cc_final: 0.8709 (mmm) REVERT: C 5035 GLN cc_start: 0.9450 (mt0) cc_final: 0.9054 (mp10) REVERT: D 127 MET cc_start: 0.8735 (tpp) cc_final: 0.8448 (tmm) REVERT: D 846 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7367 (tm) REVERT: D 924 MET cc_start: 0.6659 (ptp) cc_final: 0.6455 (tmm) REVERT: D 941 MET cc_start: 0.7393 (tpt) cc_final: 0.7140 (tpt) REVERT: D 1170 MET cc_start: 0.7979 (tpp) cc_final: 0.7755 (tpp) REVERT: D 1286 MET cc_start: 0.5986 (tpt) cc_final: 0.5634 (tpt) REVERT: D 1851 MET cc_start: 0.9000 (mmm) cc_final: 0.8750 (mmm) REVERT: D 2530 MET cc_start: 0.8601 (ppp) cc_final: 0.8083 (ppp) REVERT: D 2618 MET cc_start: 0.8736 (mpp) cc_final: 0.8067 (mpp) REVERT: D 2874 MET cc_start: -0.5623 (ptm) cc_final: -0.5830 (ptm) REVERT: D 3038 MET cc_start: 0.6565 (ppp) cc_final: 0.5337 (ptm) REVERT: D 3435 PHE cc_start: 0.8786 (t80) cc_final: 0.8281 (t80) REVERT: D 3518 LEU cc_start: 0.9550 (mt) cc_final: 0.9194 (mt) REVERT: D 3723 MET cc_start: 0.9249 (mmp) cc_final: 0.9039 (mmp) REVERT: D 4097 MET cc_start: -0.3400 (mtp) cc_final: -0.3752 (mtp) REVERT: D 4580 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7109 (t80) REVERT: D 4657 CYS cc_start: 0.8932 (m) cc_final: 0.8634 (m) REVERT: D 4880 MET cc_start: 0.9079 (tpp) cc_final: 0.8679 (tpp) REVERT: D 4954 MET cc_start: 0.9532 (tpt) cc_final: 0.9014 (mmm) REVERT: D 4965 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8548 (m) REVERT: D 5012 LYS cc_start: 0.9415 (mptt) cc_final: 0.9122 (mmtm) REVERT: D 5013 MET cc_start: 0.9097 (mtp) cc_final: 0.8709 (mmm) REVERT: D 5035 GLN cc_start: 0.9503 (mt0) cc_final: 0.9071 (mp10) REVERT: E 29 MET cc_start: 0.9079 (mtp) cc_final: 0.8446 (ttp) REVERT: F 29 MET cc_start: 0.9082 (mtp) cc_final: 0.8445 (ttp) REVERT: G 29 MET cc_start: 0.9081 (mtp) cc_final: 0.8445 (ttp) REVERT: H 29 MET cc_start: 0.9081 (mtp) cc_final: 0.8446 (ttp) outliers start: 187 outliers final: 125 residues processed: 1017 average time/residue: 1.1404 time to fit residues: 2105.9888 Evaluate side-chains 1003 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 862 time to evaluate : 10.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2256 TYR Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3638 MET Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 3701 LEU Chi-restraints excluded: chain A residue 4023 MET Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4706 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4884 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4965 SER Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 1636 MET Chi-restraints excluded: chain B residue 2170 MET Chi-restraints excluded: chain B residue 2256 TYR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3638 MET Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 3701 LEU Chi-restraints excluded: chain B residue 4023 MET Chi-restraints excluded: chain B residue 4146 LEU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4639 MET Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4965 SER Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 1636 MET Chi-restraints excluded: chain C residue 2170 MET Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2258 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3638 MET Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 3701 LEU Chi-restraints excluded: chain C residue 4023 MET Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4639 MET Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4965 SER Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 1636 MET Chi-restraints excluded: chain D residue 2170 MET Chi-restraints excluded: chain D residue 2256 TYR Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 2464 ASP Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3638 MET Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 3701 LEU Chi-restraints excluded: chain D residue 4146 LEU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4639 MET Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4965 SER Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 6.9990 chunk 688 optimal weight: 40.0000 chunk 1029 optimal weight: 2.9990 chunk 519 optimal weight: 20.0000 chunk 338 optimal weight: 10.0000 chunk 333 optimal weight: 7.9990 chunk 1095 optimal weight: 2.9990 chunk 1174 optimal weight: 6.9990 chunk 852 optimal weight: 0.9980 chunk 160 optimal weight: 0.0570 chunk 1354 optimal weight: 9.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 GLN A2247 GLN ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2487 GLN ** A2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A4216 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1631 GLN B2247 GLN ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2487 GLN ** B2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4949 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1631 GLN C2247 GLN ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4216 GLN C4949 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1631 GLN D2247 GLN ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2551 ASN ** D2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 146364 Z= 0.211 Angle : 0.697 15.879 198272 Z= 0.338 Chirality : 0.043 0.379 21792 Planarity : 0.004 0.062 25772 Dihedral : 5.548 156.952 19676 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 1.19 % Allowed : 13.04 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.38 (0.06), residues: 17844 helix: 1.17 (0.06), residues: 8720 sheet: -0.86 (0.13), residues: 1632 loop : -0.50 (0.07), residues: 7492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 200 HIS 0.008 0.001 HIS A3771 PHE 0.029 0.001 PHE C4732 TYR 0.024 0.001 TYR A2128 ARG 0.010 0.000 ARG D2575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 912 time to evaluate : 12.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 22 LEU cc_start: 0.9102 (mm) cc_final: 0.8874 (tp) REVERT: A 116 MET cc_start: 0.9230 (mmm) cc_final: 0.8716 (mmm) REVERT: A 846 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7252 (tm) REVERT: A 924 MET cc_start: 0.4254 (ptt) cc_final: 0.3750 (tmm) REVERT: A 941 MET cc_start: 0.7335 (tpt) cc_final: 0.7097 (tpt) REVERT: A 1170 MET cc_start: 0.7988 (tpp) cc_final: 0.7691 (tpp) REVERT: A 1230 MET cc_start: 0.8444 (mmm) cc_final: 0.8116 (mmm) REVERT: A 1286 MET cc_start: 0.6069 (tpt) cc_final: 0.5761 (tpt) REVERT: A 1648 MET cc_start: 0.8663 (mpp) cc_final: 0.8394 (pmm) REVERT: A 1851 MET cc_start: 0.8914 (mmm) cc_final: 0.8663 (mmm) REVERT: A 2210 VAL cc_start: 0.9695 (OUTLIER) cc_final: 0.9449 (p) REVERT: A 2211 MET cc_start: 0.9278 (mmm) cc_final: 0.9039 (mmm) REVERT: A 2267 MET cc_start: 0.7820 (tmm) cc_final: 0.7323 (tmm) REVERT: A 2530 MET cc_start: 0.8779 (ppp) cc_final: 0.8312 (ppp) REVERT: A 2618 MET cc_start: 0.8680 (mpp) cc_final: 0.7986 (mpp) REVERT: A 3038 MET cc_start: 0.6294 (ppp) cc_final: 0.4996 (ptm) REVERT: A 3435 PHE cc_start: 0.8594 (t80) cc_final: 0.7911 (t80) REVERT: A 3517 MET cc_start: 0.8832 (tpp) cc_final: 0.8496 (tpp) REVERT: A 3518 LEU cc_start: 0.9516 (mt) cc_final: 0.9199 (mt) REVERT: A 3654 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9447 (pp) REVERT: A 3720 TYR cc_start: 0.8353 (p90) cc_final: 0.8140 (p90) REVERT: A 4072 VAL cc_start: 0.4168 (m) cc_final: 0.3953 (m) REVERT: A 4097 MET cc_start: -0.3873 (mtp) cc_final: -0.4230 (mtp) REVERT: A 4580 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.6997 (t80) REVERT: A 4874 MET cc_start: 0.9191 (mmm) cc_final: 0.8888 (mmm) REVERT: A 4880 MET cc_start: 0.9095 (tpp) cc_final: 0.8709 (mpp) REVERT: A 4965 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8374 (m) REVERT: A 4969 ASP cc_start: 0.9256 (m-30) cc_final: 0.9046 (m-30) REVERT: A 5012 LYS cc_start: 0.9421 (mptt) cc_final: 0.9105 (mmtm) REVERT: A 5013 MET cc_start: 0.8992 (mtp) cc_final: 0.8620 (mmm) REVERT: A 5030 LYS cc_start: 0.9593 (ttmt) cc_final: 0.9323 (ttmm) REVERT: A 5035 GLN cc_start: 0.9461 (mt0) cc_final: 0.9050 (mp10) REVERT: B 127 MET cc_start: 0.8725 (tpp) cc_final: 0.8437 (tmm) REVERT: B 846 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7175 (tm) REVERT: B 924 MET cc_start: 0.6161 (ptp) cc_final: 0.5804 (tmm) REVERT: B 941 MET cc_start: 0.7248 (tpt) cc_final: 0.6964 (tpt) REVERT: B 1170 MET cc_start: 0.7984 (tpp) cc_final: 0.7707 (tpp) REVERT: B 1286 MET cc_start: 0.6123 (tpt) cc_final: 0.5887 (tpt) REVERT: B 1851 MET cc_start: 0.8922 (mmm) cc_final: 0.8683 (mmm) REVERT: B 2250 MET cc_start: 0.9225 (mmt) cc_final: 0.8908 (mmm) REVERT: B 2267 MET cc_start: 0.7868 (tmm) cc_final: 0.7367 (tmm) REVERT: B 2530 MET cc_start: 0.8797 (ppp) cc_final: 0.8315 (ppp) REVERT: B 2618 MET cc_start: 0.8674 (mpp) cc_final: 0.8054 (mpp) REVERT: B 2874 MET cc_start: -0.5614 (ptm) cc_final: -0.5825 (ptm) REVERT: B 3038 MET cc_start: 0.6243 (ppp) cc_final: 0.4958 (ptm) REVERT: B 3435 PHE cc_start: 0.8708 (t80) cc_final: 0.8164 (t80) REVERT: B 3518 LEU cc_start: 0.9569 (mt) cc_final: 0.9230 (mt) REVERT: B 3654 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9463 (pp) REVERT: B 4072 VAL cc_start: 0.4300 (m) cc_final: 0.4084 (m) REVERT: B 4097 MET cc_start: -0.3965 (mtp) cc_final: -0.4307 (mtp) REVERT: B 4227 GLU cc_start: 0.8517 (pm20) cc_final: 0.7782 (pp20) REVERT: B 4580 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7137 (t80) REVERT: B 4880 MET cc_start: 0.9054 (tpp) cc_final: 0.8774 (tpp) REVERT: B 4933 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8335 (mp10) REVERT: B 4953 ASP cc_start: 0.9019 (m-30) cc_final: 0.8724 (m-30) REVERT: B 5012 LYS cc_start: 0.9413 (mptt) cc_final: 0.9172 (mmtm) REVERT: B 5013 MET cc_start: 0.8982 (mtp) cc_final: 0.8635 (mmm) REVERT: B 5035 GLN cc_start: 0.9488 (mt0) cc_final: 0.9065 (mp10) REVERT: C 22 LEU cc_start: 0.9111 (mm) cc_final: 0.8908 (tp) REVERT: C 127 MET cc_start: 0.8720 (tpp) cc_final: 0.8432 (tmm) REVERT: C 846 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7178 (tm) REVERT: C 924 MET cc_start: 0.6158 (ptp) cc_final: 0.5797 (tmm) REVERT: C 941 MET cc_start: 0.7264 (tpt) cc_final: 0.6967 (tpt) REVERT: C 1170 MET cc_start: 0.7981 (tpp) cc_final: 0.7702 (tpp) REVERT: C 1286 MET cc_start: 0.6121 (tpt) cc_final: 0.5882 (tpt) REVERT: C 1648 MET cc_start: 0.8670 (mpp) cc_final: 0.8230 (pmm) REVERT: C 1851 MET cc_start: 0.8917 (mmm) cc_final: 0.8670 (mmm) REVERT: C 2250 MET cc_start: 0.9226 (mmt) cc_final: 0.8909 (mmm) REVERT: C 2267 MET cc_start: 0.7869 (tmm) cc_final: 0.7369 (tmm) REVERT: C 2530 MET cc_start: 0.8786 (ppp) cc_final: 0.8327 (ppp) REVERT: C 2618 MET cc_start: 0.8678 (mpp) cc_final: 0.8059 (mpp) REVERT: C 2874 MET cc_start: -0.5500 (ptm) cc_final: -0.5720 (ptm) REVERT: C 3038 MET cc_start: 0.6244 (ppp) cc_final: 0.4957 (ptm) REVERT: C 3435 PHE cc_start: 0.8708 (t80) cc_final: 0.8165 (t80) REVERT: C 3518 LEU cc_start: 0.9568 (mt) cc_final: 0.9229 (mt) REVERT: C 3654 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9463 (pp) REVERT: C 3720 TYR cc_start: 0.8349 (p90) cc_final: 0.8124 (p90) REVERT: C 4072 VAL cc_start: 0.4296 (m) cc_final: 0.4079 (m) REVERT: C 4097 MET cc_start: -0.3981 (mtp) cc_final: -0.4326 (mtp) REVERT: C 4580 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7148 (t80) REVERT: C 4657 CYS cc_start: 0.8705 (m) cc_final: 0.8409 (m) REVERT: C 4880 MET cc_start: 0.9054 (tpp) cc_final: 0.8777 (tpp) REVERT: C 4933 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: C 4953 ASP cc_start: 0.9042 (m-30) cc_final: 0.8746 (m-30) REVERT: C 4993 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8460 (ttp) REVERT: C 5012 LYS cc_start: 0.9414 (mptt) cc_final: 0.9172 (mmtm) REVERT: C 5013 MET cc_start: 0.8986 (mtp) cc_final: 0.8635 (mmm) REVERT: C 5035 GLN cc_start: 0.9429 (mt0) cc_final: 0.9095 (mp10) REVERT: D 22 LEU cc_start: 0.9110 (mm) cc_final: 0.8909 (tp) REVERT: D 127 MET cc_start: 0.8719 (tpp) cc_final: 0.8432 (tmm) REVERT: D 846 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7179 (tm) REVERT: D 924 MET cc_start: 0.6156 (ptp) cc_final: 0.5795 (tmm) REVERT: D 941 MET cc_start: 0.7265 (tpt) cc_final: 0.6968 (tpt) REVERT: D 1170 MET cc_start: 0.7982 (tpp) cc_final: 0.7706 (tpp) REVERT: D 1286 MET cc_start: 0.6121 (tpt) cc_final: 0.5879 (tpt) REVERT: D 1648 MET cc_start: 0.8671 (mpp) cc_final: 0.8233 (pmm) REVERT: D 1851 MET cc_start: 0.8920 (mmm) cc_final: 0.8682 (mmm) REVERT: D 2250 MET cc_start: 0.9235 (mmt) cc_final: 0.8908 (mmm) REVERT: D 2267 MET cc_start: 0.7871 (tmm) cc_final: 0.7367 (tmm) REVERT: D 2530 MET cc_start: 0.8560 (ppp) cc_final: 0.8033 (ppp) REVERT: D 2618 MET cc_start: 0.8673 (mpp) cc_final: 0.8061 (mpp) REVERT: D 2874 MET cc_start: -0.5633 (ptm) cc_final: -0.5841 (ptm) REVERT: D 3038 MET cc_start: 0.6313 (ppp) cc_final: 0.5044 (ptm) REVERT: D 3435 PHE cc_start: 0.8710 (t80) cc_final: 0.8168 (t80) REVERT: D 3518 LEU cc_start: 0.9569 (mt) cc_final: 0.9230 (mt) REVERT: D 3654 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9464 (pp) REVERT: D 4072 VAL cc_start: 0.4276 (m) cc_final: 0.4059 (m) REVERT: D 4097 MET cc_start: -0.3969 (mtp) cc_final: -0.4303 (mtp) REVERT: D 4580 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.6949 (t80) REVERT: D 4880 MET cc_start: 0.9043 (tpp) cc_final: 0.8766 (tpp) REVERT: D 4954 MET cc_start: 0.9488 (tpt) cc_final: 0.9026 (mmm) REVERT: D 5012 LYS cc_start: 0.9412 (mptt) cc_final: 0.9172 (mmtm) REVERT: D 5013 MET cc_start: 0.8985 (mtp) cc_final: 0.8635 (mmm) REVERT: D 5035 GLN cc_start: 0.9486 (mt0) cc_final: 0.9063 (mp10) REVERT: E 29 MET cc_start: 0.9004 (mtp) cc_final: 0.8519 (ttp) REVERT: F 29 MET cc_start: 0.9003 (mtp) cc_final: 0.8517 (ttp) REVERT: G 29 MET cc_start: 0.9003 (mtp) cc_final: 0.8517 (ttp) REVERT: H 29 MET cc_start: 0.9003 (mtp) cc_final: 0.8519 (ttp) outliers start: 169 outliers final: 125 residues processed: 1025 average time/residue: 1.1767 time to fit residues: 2189.2097 Evaluate side-chains 1025 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 883 time to evaluate : 12.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1636 MET Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2256 TYR Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2464 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3638 MET Chi-restraints excluded: chain A residue 3654 LEU Chi-restraints excluded: chain A residue 3673 MET Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 3701 LEU Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4884 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4965 SER Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 2170 MET Chi-restraints excluded: chain B residue 2256 TYR Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 2971 GLN Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3638 MET Chi-restraints excluded: chain B residue 3654 LEU Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 3701 LEU Chi-restraints excluded: chain B residue 4146 LEU Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4639 MET Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 2170 MET Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 2464 ASP Chi-restraints excluded: chain C residue 2971 GLN Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3638 MET Chi-restraints excluded: chain C residue 3654 LEU Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 3701 LEU Chi-restraints excluded: chain C residue 4146 LEU Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4556 SER Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4639 MET Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 2170 MET Chi-restraints excluded: chain D residue 2256 TYR Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 2971 GLN Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3638 MET Chi-restraints excluded: chain D residue 3654 LEU Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 3701 LEU Chi-restraints excluded: chain D residue 4146 LEU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4556 SER Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 20.0000 chunk 1651 optimal weight: 9.9990 chunk 1506 optimal weight: 0.9980 chunk 1605 optimal weight: 7.9990 chunk 1650 optimal weight: 0.6980 chunk 966 optimal weight: 50.0000 chunk 699 optimal weight: 0.0030 chunk 1261 optimal weight: 9.9990 chunk 492 optimal weight: 8.9990 chunk 1451 optimal weight: 7.9990 chunk 1518 optimal weight: 20.0000 overall best weight: 3.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2487 GLN ** A2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A2877 GLN A4949 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2487 GLN ** B2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D4120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 146364 Z= 0.236 Angle : 0.706 16.030 198272 Z= 0.342 Chirality : 0.043 0.379 21792 Planarity : 0.004 0.061 25772 Dihedral : 5.519 156.413 19676 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.25 % Favored : 95.73 % Rotamer: Outliers : 1.14 % Allowed : 13.22 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.39 (0.06), residues: 17844 helix: 1.17 (0.06), residues: 8760 sheet: -0.88 (0.13), residues: 1664 loop : -0.49 (0.07), residues: 7420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D4644 HIS 0.007 0.001 HIS A3771 PHE 0.034 0.002 PHE A4732 TYR 0.024 0.001 TYR A2128 ARG 0.010 0.000 ARG D2575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 892 time to evaluate : 12.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 116 MET cc_start: 0.9226 (mmm) cc_final: 0.8688 (mmm) REVERT: A 846 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7210 (tm) REVERT: A 924 MET cc_start: 0.4369 (ptt) cc_final: 0.3930 (tmm) REVERT: A 941 MET cc_start: 0.7412 (tpt) cc_final: 0.7148 (tpt) REVERT: A 1170 MET cc_start: 0.7998 (tpp) cc_final: 0.7709 (tpp) REVERT: A 1230 MET cc_start: 0.8461 (mmm) cc_final: 0.8134 (mmm) REVERT: A 1286 MET cc_start: 0.6067 (tpt) cc_final: 0.5698 (tpt) REVERT: A 1648 MET cc_start: 0.8648 (mpp) cc_final: 0.8390 (pmm) REVERT: A 1814 MET cc_start: 0.9072 (mtt) cc_final: 0.8802 (mtp) REVERT: A 1851 MET cc_start: 0.8919 (mmm) cc_final: 0.8680 (mmm) REVERT: A 2210 VAL cc_start: 0.9704 (OUTLIER) cc_final: 0.9492 (p) REVERT: A 2267 MET cc_start: 0.7869 (tmm) cc_final: 0.7378 (tmm) REVERT: A 2530 MET cc_start: 0.8762 (ppp) cc_final: 0.8380 (ppp) REVERT: A 2618 MET cc_start: 0.8673 (mpp) cc_final: 0.8041 (mpp) REVERT: A 3038 MET cc_start: 0.6335 (ppp) cc_final: 0.5051 (ptm) REVERT: A 3435 PHE cc_start: 0.8598 (t80) cc_final: 0.7882 (t80) REVERT: A 3517 MET cc_start: 0.8830 (tpp) cc_final: 0.8490 (tpp) REVERT: A 3518 LEU cc_start: 0.9462 (mt) cc_final: 0.9135 (mt) REVERT: A 3654 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9471 (pp) REVERT: A 4072 VAL cc_start: 0.4490 (m) cc_final: 0.4276 (m) REVERT: A 4097 MET cc_start: -0.4047 (mtp) cc_final: -0.4393 (mtp) REVERT: A 4580 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 4732 PHE cc_start: 0.7141 (t80) cc_final: 0.6934 (t80) REVERT: A 4874 MET cc_start: 0.9214 (mmm) cc_final: 0.8893 (mmm) REVERT: A 4880 MET cc_start: 0.9132 (tpp) cc_final: 0.8705 (mpp) REVERT: A 4949 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7949 (tp40) REVERT: A 4965 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8365 (m) REVERT: A 5012 LYS cc_start: 0.9433 (mptt) cc_final: 0.9120 (mmtm) REVERT: A 5013 MET cc_start: 0.8951 (mtp) cc_final: 0.8661 (mmm) REVERT: A 5035 GLN cc_start: 0.9464 (mt0) cc_final: 0.9048 (mp10) REVERT: B 127 MET cc_start: 0.8723 (tpp) cc_final: 0.8436 (tmm) REVERT: B 846 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7295 (tm) REVERT: B 924 MET cc_start: 0.6149 (ptp) cc_final: 0.5788 (tmm) REVERT: B 941 MET cc_start: 0.7289 (tpt) cc_final: 0.6999 (tpt) REVERT: B 1170 MET cc_start: 0.7995 (tpp) cc_final: 0.7728 (tpp) REVERT: B 1286 MET cc_start: 0.6141 (tpt) cc_final: 0.5890 (tpt) REVERT: B 1648 MET cc_start: 0.8835 (pmm) cc_final: 0.8334 (pmm) REVERT: B 1851 MET cc_start: 0.8923 (mmm) cc_final: 0.8686 (mmm) REVERT: B 2250 MET cc_start: 0.9227 (mmt) cc_final: 0.8895 (mmm) REVERT: B 2267 MET cc_start: 0.7883 (tmm) cc_final: 0.7364 (tmm) REVERT: B 2530 MET cc_start: 0.8745 (ppp) cc_final: 0.8249 (ppp) REVERT: B 2618 MET cc_start: 0.8661 (mpp) cc_final: 0.8028 (mpp) REVERT: B 2874 MET cc_start: -0.5487 (ptm) cc_final: -0.5704 (ptm) REVERT: B 3038 MET cc_start: 0.6243 (ppp) cc_final: 0.4963 (ptm) REVERT: B 3435 PHE cc_start: 0.8707 (t80) cc_final: 0.7699 (t80) REVERT: B 3517 MET cc_start: 0.8997 (mmm) cc_final: 0.8522 (tpp) REVERT: B 3518 LEU cc_start: 0.9559 (mt) cc_final: 0.9183 (mt) REVERT: B 3654 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9471 (pp) REVERT: B 4097 MET cc_start: -0.3892 (mtp) cc_final: -0.4222 (mtp) REVERT: B 4227 GLU cc_start: 0.8627 (pm20) cc_final: 0.7907 (pp20) REVERT: B 4580 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7147 (t80) REVERT: B 4657 CYS cc_start: 0.8767 (m) cc_final: 0.8463 (m) REVERT: B 4880 MET cc_start: 0.9064 (tpp) cc_final: 0.8781 (tpp) REVERT: B 4933 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: B 4953 ASP cc_start: 0.8957 (m-30) cc_final: 0.8403 (m-30) REVERT: B 5012 LYS cc_start: 0.9415 (mptt) cc_final: 0.9106 (mmtm) REVERT: B 5013 MET cc_start: 0.8966 (mtp) cc_final: 0.8653 (mmm) REVERT: B 5035 GLN cc_start: 0.9487 (mt0) cc_final: 0.9077 (mp10) REVERT: C 22 LEU cc_start: 0.9139 (mm) cc_final: 0.8910 (tp) REVERT: C 116 MET cc_start: 0.9237 (mmm) cc_final: 0.8707 (mmm) REVERT: C 127 MET cc_start: 0.8724 (tpp) cc_final: 0.8435 (tmm) REVERT: C 846 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7296 (tm) REVERT: C 924 MET cc_start: 0.6147 (ptp) cc_final: 0.5788 (tmm) REVERT: C 941 MET cc_start: 0.7286 (tpt) cc_final: 0.6995 (tpt) REVERT: C 1170 MET cc_start: 0.7993 (tpp) cc_final: 0.7724 (tpp) REVERT: C 1286 MET cc_start: 0.6137 (tpt) cc_final: 0.5889 (tpt) REVERT: C 1648 MET cc_start: 0.8663 (mpp) cc_final: 0.8215 (pmm) REVERT: C 1851 MET cc_start: 0.8921 (mmm) cc_final: 0.8683 (mmm) REVERT: C 2250 MET cc_start: 0.9227 (mmt) cc_final: 0.8894 (mmm) REVERT: C 2267 MET cc_start: 0.7882 (tmm) cc_final: 0.7366 (tmm) REVERT: C 2530 MET cc_start: 0.8713 (ppp) cc_final: 0.8330 (ppp) REVERT: C 2618 MET cc_start: 0.8662 (mpp) cc_final: 0.8031 (mpp) REVERT: C 2874 MET cc_start: -0.5510 (ptm) cc_final: -0.5710 (ptm) REVERT: C 3038 MET cc_start: 0.6241 (ppp) cc_final: 0.4961 (ptm) REVERT: C 3435 PHE cc_start: 0.8703 (t80) cc_final: 0.7697 (t80) REVERT: C 3517 MET cc_start: 0.8995 (mmm) cc_final: 0.8522 (tpp) REVERT: C 3518 LEU cc_start: 0.9557 (mt) cc_final: 0.9182 (mt) REVERT: C 3654 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9471 (pp) REVERT: C 3720 TYR cc_start: 0.8388 (p90) cc_final: 0.8171 (p90) REVERT: C 4097 MET cc_start: -0.3904 (mtp) cc_final: -0.4238 (mtp) REVERT: C 4580 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7165 (t80) REVERT: C 4657 CYS cc_start: 0.8651 (m) cc_final: 0.8371 (m) REVERT: C 4880 MET cc_start: 0.9062 (tpp) cc_final: 0.8785 (tpp) REVERT: C 4933 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: C 4993 MET cc_start: 0.8695 (mtp) cc_final: 0.8486 (ttp) REVERT: C 5012 LYS cc_start: 0.9414 (mptt) cc_final: 0.9105 (mmtm) REVERT: C 5013 MET cc_start: 0.8967 (mtp) cc_final: 0.8650 (mmm) REVERT: C 5035 GLN cc_start: 0.9390 (mt0) cc_final: 0.9025 (mp10) REVERT: D 22 LEU cc_start: 0.9117 (mm) cc_final: 0.8899 (tp) REVERT: D 116 MET cc_start: 0.9233 (mmm) cc_final: 0.8704 (mmm) REVERT: D 127 MET cc_start: 0.8722 (tpp) cc_final: 0.8435 (tmm) REVERT: D 846 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7298 (tm) REVERT: D 924 MET cc_start: 0.6146 (ptp) cc_final: 0.5786 (tmm) REVERT: D 941 MET cc_start: 0.7287 (tpt) cc_final: 0.6997 (tpt) REVERT: D 1170 MET cc_start: 0.7994 (tpp) cc_final: 0.7725 (tpp) REVERT: D 1286 MET cc_start: 0.6127 (tpt) cc_final: 0.5878 (tpt) REVERT: D 1648 MET cc_start: 0.8663 (mpp) cc_final: 0.8216 (pmm) REVERT: D 1851 MET cc_start: 0.8920 (mmm) cc_final: 0.8686 (mmm) REVERT: D 2250 MET cc_start: 0.9227 (mmt) cc_final: 0.8896 (mmm) REVERT: D 2267 MET cc_start: 0.7886 (tmm) cc_final: 0.7366 (tmm) REVERT: D 2490 MET cc_start: 0.7905 (mmt) cc_final: 0.7569 (mmt) REVERT: D 2530 MET cc_start: 0.8591 (ppp) cc_final: 0.8064 (ppp) REVERT: D 2618 MET cc_start: 0.8671 (mpp) cc_final: 0.8032 (mpp) REVERT: D 2874 MET cc_start: -0.5506 (ptm) cc_final: -0.5708 (ptm) REVERT: D 3038 MET cc_start: 0.6243 (ppp) cc_final: 0.4961 (ptm) REVERT: D 3435 PHE cc_start: 0.8707 (t80) cc_final: 0.7702 (t80) REVERT: D 3517 MET cc_start: 0.8997 (mmm) cc_final: 0.8523 (tpp) REVERT: D 3518 LEU cc_start: 0.9559 (mt) cc_final: 0.9183 (mt) REVERT: D 3654 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9472 (pp) REVERT: D 4097 MET cc_start: -0.3889 (mtp) cc_final: -0.4229 (mtp) REVERT: D 4580 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.6973 (t80) REVERT: D 4657 CYS cc_start: 0.8745 (m) cc_final: 0.8453 (m) REVERT: D 4880 MET cc_start: 0.9055 (tpp) cc_final: 0.8774 (tpp) REVERT: D 4954 MET cc_start: 0.9458 (tpt) cc_final: 0.8998 (mmm) REVERT: D 5012 LYS cc_start: 0.9413 (mptt) cc_final: 0.9105 (mmtm) REVERT: D 5013 MET cc_start: 0.8967 (mtp) cc_final: 0.8647 (mmm) REVERT: D 5035 GLN cc_start: 0.9485 (mt0) cc_final: 0.9075 (mp10) REVERT: E 29 MET cc_start: 0.9014 (mtp) cc_final: 0.8471 (ttp) REVERT: F 29 MET cc_start: 0.9013 (mtp) cc_final: 0.8470 (ttp) REVERT: G 29 MET cc_start: 0.9012 (mtp) cc_final: 0.8468 (ttp) REVERT: H 29 MET cc_start: 0.9014 (mtp) cc_final: 0.8471 (ttp) outliers start: 158 outliers final: 132 residues processed: 994 average time/residue: 1.1499 time to fit residues: 2088.1219 Evaluate side-chains 1027 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 878 time to evaluate : 12.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1636 MET Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2210 VAL Chi-restraints excluded: chain A residue 2256 TYR Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2464 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2971 GLN Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3638 MET Chi-restraints excluded: chain A residue 3654 LEU Chi-restraints excluded: chain A residue 3673 MET Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 3701 LEU Chi-restraints excluded: chain A residue 3793 MET Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4706 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4884 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4965 SER Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 2170 MET Chi-restraints excluded: chain B residue 2256 TYR Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 2971 GLN Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3638 MET Chi-restraints excluded: chain B residue 3654 LEU Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 3701 LEU Chi-restraints excluded: chain B residue 4146 LEU Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4639 MET Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 2170 MET Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 2464 ASP Chi-restraints excluded: chain C residue 2971 GLN Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3638 MET Chi-restraints excluded: chain C residue 3654 LEU Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 3701 LEU Chi-restraints excluded: chain C residue 4146 LEU Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4639 MET Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 2170 MET Chi-restraints excluded: chain D residue 2256 TYR Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 2464 ASP Chi-restraints excluded: chain D residue 2971 GLN Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3638 MET Chi-restraints excluded: chain D residue 3654 LEU Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 3701 LEU Chi-restraints excluded: chain D residue 3793 MET Chi-restraints excluded: chain D residue 4146 LEU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4639 MET Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 7.9990 chunk 1054 optimal weight: 4.9990 chunk 1698 optimal weight: 10.0000 chunk 1036 optimal weight: 3.9990 chunk 805 optimal weight: 4.9990 chunk 1180 optimal weight: 4.9990 chunk 1781 optimal weight: 5.9990 chunk 1639 optimal weight: 20.0000 chunk 1418 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 1095 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2487 GLN ** A2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** A2877 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 146364 Z= 0.269 Angle : 0.727 15.988 198272 Z= 0.354 Chirality : 0.043 0.403 21792 Planarity : 0.004 0.064 25772 Dihedral : 5.569 156.184 19676 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 1.15 % Allowed : 13.35 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.35 (0.06), residues: 17844 helix: 1.11 (0.06), residues: 8788 sheet: -0.79 (0.13), residues: 1584 loop : -0.52 (0.07), residues: 7472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D4644 HIS 0.007 0.001 HIS A2253 PHE 0.027 0.002 PHE A4732 TYR 0.025 0.001 TYR A2128 ARG 0.010 0.000 ARG D2575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35688 Ramachandran restraints generated. 17844 Oldfield, 0 Emsley, 17844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 892 time to evaluate : 12.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 116 MET cc_start: 0.9186 (mmm) cc_final: 0.8624 (mmm) REVERT: A 846 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7110 (tm) REVERT: A 924 MET cc_start: 0.4786 (ptt) cc_final: 0.4361 (tmm) REVERT: A 941 MET cc_start: 0.7413 (tpt) cc_final: 0.7138 (tpt) REVERT: A 1170 MET cc_start: 0.7971 (tpp) cc_final: 0.7699 (tpp) REVERT: A 1230 MET cc_start: 0.8447 (mmm) cc_final: 0.8116 (mmm) REVERT: A 1286 MET cc_start: 0.6136 (tpt) cc_final: 0.5767 (tpt) REVERT: A 1648 MET cc_start: 0.8645 (mpp) cc_final: 0.8382 (pmm) REVERT: A 1814 MET cc_start: 0.9113 (mtt) cc_final: 0.8747 (mtp) REVERT: A 1851 MET cc_start: 0.8958 (mmm) cc_final: 0.8739 (mmm) REVERT: A 2267 MET cc_start: 0.7874 (tmm) cc_final: 0.7367 (tmm) REVERT: A 2530 MET cc_start: 0.8723 (ppp) cc_final: 0.8336 (ppp) REVERT: A 2618 MET cc_start: 0.8669 (mpp) cc_final: 0.7971 (mpp) REVERT: A 3038 MET cc_start: 0.6372 (ppp) cc_final: 0.5125 (ptm) REVERT: A 3435 PHE cc_start: 0.8597 (t80) cc_final: 0.7896 (t80) REVERT: A 3517 MET cc_start: 0.8824 (tpp) cc_final: 0.8488 (tpp) REVERT: A 3518 LEU cc_start: 0.9418 (mt) cc_final: 0.9045 (mt) REVERT: A 3654 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9520 (pp) REVERT: A 4097 MET cc_start: -0.4003 (mtp) cc_final: -0.4327 (mtp) REVERT: A 4580 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7001 (t80) REVERT: A 4732 PHE cc_start: 0.7311 (t80) cc_final: 0.7034 (t80) REVERT: A 4874 MET cc_start: 0.9140 (mmm) cc_final: 0.8827 (mmm) REVERT: A 4880 MET cc_start: 0.9141 (tpp) cc_final: 0.8736 (mpp) REVERT: A 4954 MET cc_start: 0.9494 (tpt) cc_final: 0.9147 (mmm) REVERT: A 4965 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8681 (m) REVERT: A 5012 LYS cc_start: 0.9442 (mptt) cc_final: 0.9131 (mmtm) REVERT: A 5013 MET cc_start: 0.8950 (mtp) cc_final: 0.8662 (mmm) REVERT: A 5035 GLN cc_start: 0.9475 (mt0) cc_final: 0.9100 (mp10) REVERT: B 116 MET cc_start: 0.9219 (mmm) cc_final: 0.8690 (mmm) REVERT: B 127 MET cc_start: 0.8720 (tpp) cc_final: 0.8436 (tmm) REVERT: B 846 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7228 (tm) REVERT: B 924 MET cc_start: 0.5975 (ptp) cc_final: 0.5597 (tmm) REVERT: B 941 MET cc_start: 0.7503 (tpt) cc_final: 0.7239 (tpt) REVERT: B 1170 MET cc_start: 0.8023 (tpp) cc_final: 0.7758 (tpp) REVERT: B 1286 MET cc_start: 0.6197 (tpt) cc_final: 0.5947 (tpt) REVERT: B 1648 MET cc_start: 0.8854 (pmm) cc_final: 0.8331 (pmm) REVERT: B 1851 MET cc_start: 0.8956 (mmm) cc_final: 0.8742 (mmm) REVERT: B 2250 MET cc_start: 0.9232 (mmt) cc_final: 0.8890 (mmm) REVERT: B 2267 MET cc_start: 0.7904 (tmm) cc_final: 0.7389 (tmm) REVERT: B 2530 MET cc_start: 0.8729 (ppp) cc_final: 0.8338 (ppp) REVERT: B 2618 MET cc_start: 0.8677 (mpp) cc_final: 0.8030 (mpp) REVERT: B 2874 MET cc_start: -0.5479 (ptm) cc_final: -0.5693 (ptm) REVERT: B 3038 MET cc_start: 0.6284 (ppp) cc_final: 0.5019 (ptm) REVERT: B 3435 PHE cc_start: 0.8742 (t80) cc_final: 0.7763 (t80) REVERT: B 3517 MET cc_start: 0.8970 (mmm) cc_final: 0.8484 (tpp) REVERT: B 3518 LEU cc_start: 0.9539 (mt) cc_final: 0.9146 (mt) REVERT: B 3654 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9518 (pp) REVERT: B 4097 MET cc_start: -0.3829 (mtp) cc_final: -0.4163 (mtp) REVERT: B 4227 GLU cc_start: 0.8692 (pm20) cc_final: 0.7917 (pp20) REVERT: B 4580 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7185 (t80) REVERT: B 4657 CYS cc_start: 0.8787 (m) cc_final: 0.8490 (m) REVERT: B 4880 MET cc_start: 0.9078 (tpp) cc_final: 0.8805 (tpp) REVERT: B 4953 ASP cc_start: 0.8845 (m-30) cc_final: 0.8422 (m-30) REVERT: B 5012 LYS cc_start: 0.9420 (mptt) cc_final: 0.9116 (mmtm) REVERT: B 5013 MET cc_start: 0.8965 (mtp) cc_final: 0.8629 (mmm) REVERT: B 5035 GLN cc_start: 0.9488 (mt0) cc_final: 0.9079 (mp10) REVERT: C 22 LEU cc_start: 0.9076 (mm) cc_final: 0.8866 (tp) REVERT: C 116 MET cc_start: 0.9220 (mmm) cc_final: 0.8689 (mmm) REVERT: C 127 MET cc_start: 0.8720 (tpp) cc_final: 0.8434 (tmm) REVERT: C 846 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7230 (tm) REVERT: C 924 MET cc_start: 0.5969 (ptp) cc_final: 0.5592 (tmm) REVERT: C 941 MET cc_start: 0.7615 (tpt) cc_final: 0.7350 (tpt) REVERT: C 1170 MET cc_start: 0.8019 (tpp) cc_final: 0.7754 (tpp) REVERT: C 1286 MET cc_start: 0.6190 (tpt) cc_final: 0.5942 (tpt) REVERT: C 1648 MET cc_start: 0.8683 (mpp) cc_final: 0.8234 (pmm) REVERT: C 1851 MET cc_start: 0.8955 (mmm) cc_final: 0.8738 (mmm) REVERT: C 2250 MET cc_start: 0.9231 (mmt) cc_final: 0.8891 (mmm) REVERT: C 2267 MET cc_start: 0.7904 (tmm) cc_final: 0.7387 (tmm) REVERT: C 2530 MET cc_start: 0.8728 (ppp) cc_final: 0.8349 (ppp) REVERT: C 2618 MET cc_start: 0.8675 (mpp) cc_final: 0.8030 (mpp) REVERT: C 2874 MET cc_start: -0.5618 (ptm) cc_final: -0.5826 (ptm) REVERT: C 3038 MET cc_start: 0.6281 (ppp) cc_final: 0.5016 (ptm) REVERT: C 3435 PHE cc_start: 0.8738 (t80) cc_final: 0.7755 (t80) REVERT: C 3517 MET cc_start: 0.8969 (mmm) cc_final: 0.8487 (tpp) REVERT: C 3518 LEU cc_start: 0.9537 (mt) cc_final: 0.9145 (mt) REVERT: C 3654 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9518 (pp) REVERT: C 3720 TYR cc_start: 0.8435 (p90) cc_final: 0.8223 (p90) REVERT: C 4097 MET cc_start: -0.3845 (mtp) cc_final: -0.4176 (mtp) REVERT: C 4580 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7201 (t80) REVERT: C 4657 CYS cc_start: 0.8668 (m) cc_final: 0.8399 (m) REVERT: C 4880 MET cc_start: 0.9076 (tpp) cc_final: 0.8803 (tpp) REVERT: C 4953 ASP cc_start: 0.9030 (m-30) cc_final: 0.8698 (m-30) REVERT: C 4993 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8519 (ttp) REVERT: C 5012 LYS cc_start: 0.9421 (mptt) cc_final: 0.9116 (mmtm) REVERT: C 5013 MET cc_start: 0.8965 (mtp) cc_final: 0.8625 (mmm) REVERT: D 22 LEU cc_start: 0.9076 (mm) cc_final: 0.8868 (tp) REVERT: D 116 MET cc_start: 0.9218 (mmm) cc_final: 0.8686 (mmm) REVERT: D 127 MET cc_start: 0.8719 (tpp) cc_final: 0.8434 (tmm) REVERT: D 846 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7231 (tm) REVERT: D 924 MET cc_start: 0.5964 (ptp) cc_final: 0.5589 (tmm) REVERT: D 941 MET cc_start: 0.7618 (tpt) cc_final: 0.7354 (tpt) REVERT: D 1170 MET cc_start: 0.8022 (tpp) cc_final: 0.7756 (tpp) REVERT: D 1286 MET cc_start: 0.6187 (tpt) cc_final: 0.5938 (tpt) REVERT: D 1648 MET cc_start: 0.8684 (mpp) cc_final: 0.8235 (pmm) REVERT: D 1851 MET cc_start: 0.8956 (mmm) cc_final: 0.8743 (mmm) REVERT: D 2250 MET cc_start: 0.9232 (mmt) cc_final: 0.8890 (mmm) REVERT: D 2267 MET cc_start: 0.7909 (tmm) cc_final: 0.7392 (tmm) REVERT: D 2490 MET cc_start: 0.7999 (mmt) cc_final: 0.7574 (mmt) REVERT: D 2530 MET cc_start: 0.8611 (ppp) cc_final: 0.8082 (ppp) REVERT: D 2618 MET cc_start: 0.8698 (mpp) cc_final: 0.8073 (mpp) REVERT: D 2874 MET cc_start: -0.5619 (ptm) cc_final: -0.5829 (ptm) REVERT: D 3038 MET cc_start: 0.6285 (ppp) cc_final: 0.5020 (ptm) REVERT: D 3435 PHE cc_start: 0.8741 (t80) cc_final: 0.7761 (t80) REVERT: D 3517 MET cc_start: 0.8969 (mmm) cc_final: 0.8487 (tpp) REVERT: D 3518 LEU cc_start: 0.9544 (mt) cc_final: 0.9154 (mt) REVERT: D 3654 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9519 (pp) REVERT: D 4097 MET cc_start: -0.3834 (mtp) cc_final: -0.4157 (mtp) REVERT: D 4580 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7002 (t80) REVERT: D 4657 CYS cc_start: 0.8764 (m) cc_final: 0.8482 (m) REVERT: D 4880 MET cc_start: 0.9070 (tpp) cc_final: 0.8798 (tpp) REVERT: D 4954 MET cc_start: 0.9496 (tpt) cc_final: 0.9086 (mmm) REVERT: D 4989 MET cc_start: 0.9212 (tmm) cc_final: 0.9001 (tmm) REVERT: D 4993 MET cc_start: 0.8982 (ttp) cc_final: 0.8761 (ptm) REVERT: D 5012 LYS cc_start: 0.9420 (mptt) cc_final: 0.9115 (mmtm) REVERT: D 5013 MET cc_start: 0.8965 (mtp) cc_final: 0.8624 (mmm) REVERT: D 5035 GLN cc_start: 0.9486 (mt0) cc_final: 0.9079 (mp10) REVERT: E 29 MET cc_start: 0.9031 (mtp) cc_final: 0.8420 (ttp) REVERT: F 29 MET cc_start: 0.9033 (mtp) cc_final: 0.8419 (ttp) REVERT: G 29 MET cc_start: 0.9030 (mtp) cc_final: 0.8419 (ttp) REVERT: H 29 MET cc_start: 0.9031 (mtp) cc_final: 0.8421 (ttp) outliers start: 158 outliers final: 140 residues processed: 996 average time/residue: 1.1646 time to fit residues: 2116.9209 Evaluate side-chains 1040 residues out of total 15552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 886 time to evaluate : 12.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1462 MET Chi-restraints excluded: chain A residue 1636 MET Chi-restraints excluded: chain A residue 2170 MET Chi-restraints excluded: chain A residue 2256 TYR Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2451 LEU Chi-restraints excluded: chain A residue 2464 ASP Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2971 GLN Chi-restraints excluded: chain A residue 3531 ASP Chi-restraints excluded: chain A residue 3638 MET Chi-restraints excluded: chain A residue 3654 LEU Chi-restraints excluded: chain A residue 3673 MET Chi-restraints excluded: chain A residue 3690 VAL Chi-restraints excluded: chain A residue 3701 LEU Chi-restraints excluded: chain A residue 4146 LEU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4556 SER Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4639 MET Chi-restraints excluded: chain A residue 4651 THR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4706 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4884 LEU Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4965 SER Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 1462 MET Chi-restraints excluded: chain B residue 2170 MET Chi-restraints excluded: chain B residue 2256 TYR Chi-restraints excluded: chain B residue 2258 LEU Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2451 LEU Chi-restraints excluded: chain B residue 2464 ASP Chi-restraints excluded: chain B residue 2971 GLN Chi-restraints excluded: chain B residue 3531 ASP Chi-restraints excluded: chain B residue 3638 MET Chi-restraints excluded: chain B residue 3654 LEU Chi-restraints excluded: chain B residue 3690 VAL Chi-restraints excluded: chain B residue 3701 LEU Chi-restraints excluded: chain B residue 4146 LEU Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4556 SER Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4639 MET Chi-restraints excluded: chain B residue 4651 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1462 MET Chi-restraints excluded: chain C residue 2170 MET Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2258 LEU Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2451 LEU Chi-restraints excluded: chain C residue 2464 ASP Chi-restraints excluded: chain C residue 2971 GLN Chi-restraints excluded: chain C residue 3531 ASP Chi-restraints excluded: chain C residue 3638 MET Chi-restraints excluded: chain C residue 3654 LEU Chi-restraints excluded: chain C residue 3690 VAL Chi-restraints excluded: chain C residue 3701 LEU Chi-restraints excluded: chain C residue 4146 LEU Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4639 MET Chi-restraints excluded: chain C residue 4651 THR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 4993 MET Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 1462 MET Chi-restraints excluded: chain D residue 2170 MET Chi-restraints excluded: chain D residue 2256 TYR Chi-restraints excluded: chain D residue 2258 LEU Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2451 LEU Chi-restraints excluded: chain D residue 2464 ASP Chi-restraints excluded: chain D residue 2971 GLN Chi-restraints excluded: chain D residue 3531 ASP Chi-restraints excluded: chain D residue 3638 MET Chi-restraints excluded: chain D residue 3654 LEU Chi-restraints excluded: chain D residue 3690 VAL Chi-restraints excluded: chain D residue 3701 LEU Chi-restraints excluded: chain D residue 4146 LEU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4639 MET Chi-restraints excluded: chain D residue 4651 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 1.9990 chunk 1126 optimal weight: 0.4980 chunk 1510 optimal weight: 10.0000 chunk 434 optimal weight: 0.1980 chunk 1307 optimal weight: 0.9990 chunk 209 optimal weight: 0.3980 chunk 394 optimal weight: 6.9990 chunk 1420 optimal weight: 0.9990 chunk 594 optimal weight: 3.9990 chunk 1458 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1693 GLN ** A2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2487 GLN A2551 ASN ** A2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4949 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1693 GLN ** B2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B2877 GLN ** B3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4216 GLN ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1693 GLN ** C2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2551 ASN ** C2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** C2877 GLN ** C3456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1693 GLN ** D2349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2551 ASN ** D2584 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** D2877 GLN D4216 GLN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.073751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.054102 restraints weight = 2194755.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.054291 restraints weight = 966900.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.054509 restraints weight = 609846.743| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 146364 Z= 0.166 Angle : 0.703 16.395 198272 Z= 0.335 Chirality : 0.043 0.399 21792 Planarity : 0.004 0.058 25772 Dihedral : 5.416 157.541 19673 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 0.90 % Allowed : 13.71 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: 0.50 (0.06), residues: 17844 helix: 1.25 (0.06), residues: 8736 sheet: -0.62 (0.13), residues: 1652 loop : -0.46 (0.07), residues: 7456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D4644 HIS 0.010 0.001 HIS A3998 PHE 0.030 0.001 PHE A2973 TYR 0.022 0.001 TYR A4080 ARG 0.011 0.000 ARG A4736 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37869.58 seconds wall clock time: 661 minutes 39.41 seconds (39699.41 seconds total)